GapOverlap

From genomewiki
Jump to: navigation, search

methods

The measurements are taken from the gapOverlap.bed[.gz] file in /hive/data/genomes/<db>/bed/gapOverlap/gapOverlap.bed[.gz] The score column in the bed file (column 5) is the size of the duplicated sequence. The gap size between the duplicated sequence is calculated from: end - start + 2 * score

The size of the duplicated sequence is between 30 bases and 1000 bases, we are not checking for sizes outside that range.

The item total is the sum of the sizes of the duplicated sequences. Not both sides though, just one side. This indicates how much sequence is duplicated. Multiply this by 2 to see total amount of sequence involved in these repeats for both sides.

The gap total is the sum of the sizes of all the gaps involved.

table features

The table columns can be sorted, click on the up/down arrow icon in the column header. The 'year' is what we have in the dbDb table as indicated from the assembly information files for the date of the assembly. A few do not have dates (set to 1880), and do not have database genome browsers.

The example item is a worst case example, where the ratio of duplicate sequence size to gap size is the highest, i.e. smallest gap with largest dup size These ends were found by taking 1,000 bases on each side of any run of N's in the sequence, thus any gap, and aligned with the blat command:

 blat -q=dna -minIdentity=95 -repMatch=10 upstream.fa downstream.fa

Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence before the gap and begins exactly at the start of the downstream sequence after the gap.


gapOverlap table statistics

count year dbName ncbiAsmId assembly method item

count

item

median

item

total

gap

median

gap

total

example item

dup size, gap size, link

scatter plot

dup size vs. gap size

001 2016 CBA_J GCA_001624475.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 24180 279.5 7933814 26 26736971 999, 1, chr16:100093490-100095488 plot GCA_001624475.1_CBA_J_v1
002 2016 PAHARI_EIJ GCA_900095145.1 tbd 6365 69 479534 1 675789 1000, 1, chr7:107557946-107559946 plot GCA_900095145.1_PAHARI_EIJ_v1
003 2016 PWK_PhJ GCA_001624775.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 246352 65 16823451 25 10585326 1000, 11, chrX:47500642-47502652 plot GCA_001624775.1_PWK_PhJ_v1
004 2016 SPRET_EiJ GCA_001624865.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail genomics v. August-2015; Ragout v. 2.0b 17567 516 8157541 100 12022683 1000, 1, chr10:66049175-66051175 plot GCA_001624865.1_SPRET_EiJ_v1
005 2016 NZO_HlLtJ GCA_001624745.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 21209 448 8647582 25 14665906 1000, 1, chr10:29328015-29330015 plot GCA_001624745.1_NZO_HlLtJ_v1
006 2016 129S1_SvImJ GCA_001624185.1 SGA v. 0.9.19; Ragout v. 2.0b 20479 400 7813478 25 15456883 1000, 1, chr15:34994444-34996444 plot GCA_001624185.1_129S1_SvImJ_v1
007 2016 C57BL_6NJ GCA_001632555.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 24698 97 6239791 25 14404336 992, 1, chr10:109927459-109929443 plot GCA_001632555.1_C57BL_6NJ_v1
008 2016 AKR_J GCA_001624295.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 18106 335 6717178 25 14468858 1000, 1, chr16:53464467-53466467 plot GCA_001624295.1_AKR_J_v1
009 2016 C3H_HeJ GCA_001632575.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 19436 307 6287513 26 12931709 1000, 1, chr1:52782023-52784023 plot GCA_001632575.1_C3H_HeJ_v1
010 2016 FVB_NJ GCA_001624535.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 14811 355 4902432 11 8504942 1000, 1, chr17:22790916-22792916 plot GCA_001624535.1_FVB_NJ_v1
011 2016 WSB_EiJ GCA_001624835.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 11455 236 3524308 25 10785288 994, 1, chrX:58921651-58923639 plot GCA_001624835.1_WSB_EiJ_v1
012 2016 A_J GCA_001624215.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 38843 80 6428892 25 14025482 1000, 1, chr17:63064911-63066911 plot GCA_001624215.1_A_J_v1
013 2016 CAROLI_EIJ GCA_900094665.1 tbd 6469 70 484857 1 599072 945, 1, chr1:145228793-145230683 plot GCA_900094665.1_CAROLI_EIJ_v1
014 2016 LP_J GCA_001632615.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 18175 98 5185817 25 13674278 997, 1, chr12:42758762-42760756 plot GCA_001632615.1_LP_J_v1
015 2016 BALB_cJ GCA_001632525.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 15793 363 5543975 25 10053337 999, 1, chr4:59636957-59638955 plot GCA_001632525.1_BALB_cJ_v1
016 2016 DBA_2J GCA_001624505.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 13245 98 3606947 25 7251641 999, 1, chr10:47277903-47279901 plot GCA_001624505.1_DBA_2J_v1
017 2016 NOD_ShiLtJ GCA_001624675.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Ragout v. 2.0b 36838 172 10515906 26 25076950 1000, 1, chr15:69777938-69779938 plot GCA_001624675.1_NOD_ShiLtJ_v1
018 2016 CAST_EiJ GCA_001624445.1 SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail Genomics v. August-2015; Ragout v. 2.0b 14714 324 5063290 100 10013826 1000, 1, chr12:100100159-100102159 plot GCA_001624445.1_CAST_EiJ_v1
019 2013 CHM1 GCF_000306695.2 SRPRISM v. 2.4.28-alpha; ARGO v. 0.1 85 86 10897 88 65164 319, 10, chr6:108876987-108877634 plot CHM1
020 2018 GRCm38B tbd tbd 3 304 860 6000 57759 477, 1759, chrX_GPS_017319198v1_random:240297-243009 plot GRCm38B
021 2014 acaChl1 GCF_000695815.1 SOAPdenovo v. 1.6 5 170 1250 188 2340 722, 188, KK833582:5976-7607 plot acaChl1
024 2009 ailMel1 GCF_000004335.2 tbd 48 104 10594 1193 82504 75, 1, GL192694.1:348745-348895 plot ailMel1
025 2012 allMis1 GCF_000281125.1 Allpaths v. R41313; manual scaffolding 1151 83 273934 1 74939 999, 1, JH739280:136433-138431 plot allMis1
026 2013 allSin1 GCF_000455745.1 SOAPdenovo v. 1.05 95 125 26114 2265 261774 69, 10, KE696011:2095494-2095641 plot allSin1
027 2013 amaVit1 GCA_000332375.1 Ray software v. 3 10099 81 1392334 172 2756641 492, 13, KB238901:2710-3706 plot amaVit1
028 2013 anaPla1 GCF_000355885.1 SOAPdenovo Release v. 1.03 31 251 10663 1660 94318 99, 1, KB742632:907264-907462 plot anaPla1
029 2014 ancCey1 GCA_000688135.1 Velvet v. 1.2.05; BGI GapCloser v. 1.12 (release_2011); HaploMerger v. 20111230; ERANGE v. 3.2 805 154 171926 1 85569 981, 1, JARK01000206v1:43215-45177 plot ancCey1
030 2014 angJap1 GCA_000470695.1 CLC NGS Cell v. 3.2; CLC NGS Cell v. 4.0beta 4539 91 477038 1 610535 588, 1, KI304555:142639-143815 plot angJap1
031 2007 anoCar1 tbd tbd 20 383.5 8167 537.5 23338 965, 100, scaffold_84:3853690-3855719 plot anoCar1
032 2010 anoCar2 GCF_000090745.1 Arachne v. 3.0.0 25 240 6694 258 26105 318, 100, chr4:54548520-54549255 plot anoCar2
033 2003 anoGam1 tbd tbd 7 528 3139 1000 21041 1000, 384, chr2L:5019927-5022310 plot anoGam1
034 2006 anoGam3 GCF_000005575.2 tbd 6 415 2611 1884.5 20042 1000, 384, chr2L:5538027-5540410 plot anoGam3
035 2017 aotNan1 GCF_000952055.2 PBJelly2 v. 14.9.9; AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2 2334 182.5 863402 100 2688526 990, 10, NW_018504266v1:1888714-1890703 plot aotNan1
036 2013 apaSpi1 GCA_000385615.1 SOAPdenovo v. 1.0.5 607 61 34340 100 56961 86, 10, KB929338:2579176-2579357 plot apaSpi1
038 2004 apiMel1 tbd tbd 216 50 12150 10 24454 64, 1, Group14.17:517485-517613 plot apiMel1
039 2005 apiMel2 tbd tbd 133 50 7371 50 19757 168, 50, Group4:4855105-4855490 plot apiMel2
040 2005 apiMel3 tbd tbd 199 62 16045 50 27354 198, 50, Group15:1672512-1672957 plot apiMel3
041 2010 apiMel4 GCF_000002195.4 Atlas assembly system v. before 2011 226 52.5 13378 50 24561 167, 50, Group14:1674117-1674500 plot apiMel4
042 2008 aplCal1 tbd tbd 25 77 3383 100 16863 390, 100, scaffold_1802:24095-24974 plot aplCal1
043 2014 aptFor1 GCF_000699145.1 SOAPdenovo v. 1.6 109 147 26798 1575 323838 779, 98, KL225582:135043-136698 plot aptFor1
044 2015 aptMan1 GCF_001039765.1 tbd 15742 124 4653010 1 3331011 1000, 1, NW_013987125v1:2508272-2510272 plot aptMan1
045 2014 aquChr1 GCA_000696035.1 ABySS v. 1.3.6 4592 43 201248 65 16118238 65, 1, KK850461:8872-9002 plot aquChr1
046 2014 aquChr2 GCA_000766835.1 AllPaths-LG v. August 2013 326 82.5 31349 1 143600 1000, 1, KN265664v1:16826772-16828772 plot aquChr2
047 2013 araMac1 GCA_000400695.1 CLC Genomics Workbench v. 4.9 120 48.5 7929 33 27135 241, 2, KE047968:4314-4797 plot araMac1
048 1880 araTha1 GCF_000001735.3 tbd 1 289 289 60 60 289, 60, chr3:13855281-13855918 plot araTha1
049 2012 ascSuu1 GCA_000298755.1 SOAPdenovo v. 1.04 9 404 3688 555 6481 1000, 247, JH879107v1:69728-71974 plot ascSuu1
051 2013 astMex1 GCF_000372685.1 AllPathsLG v. Jan-2013 1385 78 137888 100 1964877 647, 1, KB872443:19678-20972 plot astMex1
052 2013 balAcu1 GCF_000493695.1 SOAPdenovo v. 16-Mar-2012 211 149 57860 821 371511 926, 15, KI537556:2252563-2254429 plot balAcu1
053 2014 balPav1 GCA_000709895.1 SOAPdenovo v. 1.6 5 270 1303 216 1098 391, 46, KL482982:8685-9512 plot balPav1
054 2014 bisBis1 GCA_000754665.1 MaSuRCA v. 2.1.0 8184 72 712109 100 947641 933, 100, KN265089v1:519297-521262 plot bisBis1
056 2011 bosMut1 GCA_000298355.1 SOAPdenovo v. 1.14 139 83 27917 1274 256420 71, 14, JH880933:479978-480133 plot bosMut1
057 2004 bosTau1 tbd tbd 6550 40 289123 50 609155 200, 50, SCAFFOLD51732:9156-9605 plot bosTau1
058 2005 bosTau2 tbd tbd 4361 105 564259 50 2525381 997, 50, scaffold4383:34413-36456 plot bosTau2
059 2006 bosTau3 tbd tbd 411 51 38673 50 270212 1000, 50, chr10:68862764-68864813 plot bosTau3
060 2007 bosTau4 tbd tbd 437 53 52814 50 376407 1000, 50, chr10:75537624-75539673 plot bosTau4
061 2009 bosTau5 tbd tbd 435 53 51742 50 376650 1000, 50, chr10:75464684-75466733 plot bosTau5
062 2009 bosTau6 GCF_000003055.5 UMD Overlapper v. 2009; additional processing 789 670 463109 100 87080 923, 1, chr22:31476636-31478482 plot bosTau6
063 2011 bosTau7 tbd tbd 413 55 39706 50 141131 1000, 50, chr10:75201034-75203083 plot bosTau7
064 2014 bosTau8 GCF_000003055.5 UMD Overlapper v. 2009; additional processing 789 670 463109 100 87080 923, 1, chr22:31476636-31478482 plot bosTau8
065 2018 bosTau9 GCF_002263795.1 Falcon v. FEB-2016 1 75 75 25 25 75, 25, chr13:11061714-11061888 plot bosTau9
066 2009 bosTauMd3 tbd tbd 789 670 463109 100 87080 923, 1, chr22:31476636-31478482 plot bosTauMd3
067 2006 braFlo1 tbd tbd 31 484 14260 417 12668 375, 1, chrUn:879323570-879324320 plot braFlo1
068 2008 braFlo2 tbd tbd 22 439 8529 411 9064 36, 1, Bf_V2_248:1229532-1229604 plot braFlo2
069 1880 braRap1 GCF_000309985.1 SOAPdenovo v. 1.04 12 104 3193 2810 47557 587, 472, chrUn_JH977260:73788-75433 plot braRap1
070 2007 bruMal1 tbd tbd 55 50 6093 1 18780 87, 1, Bmal_supercontig14387:293-467 plot bruMal1
071 2014 bruMal2 tbd tbd 46 124.5 12221 431.5 63506 1000, 20, Bmal_v3_scaffold83:22898-24917 plot bruMal2
072 2013 bubBub1 GCF_000471725.1 MaSuRCA v. 1.8.3 2383 163 395268 100 251657 990, 100, KI418684:2409965-2412044 plot bubBub1
073 2014 bucRhi1 GCF_000710305.1 SOAPdenovo v. 1.6 31 114 5089 78 3263 327, 10, KL526600:8925-9588 plot bucRhi1
075 2011 burXyl1 tbd tbd 65 601 33110 301 19553 977, 300, scaffold00460:102617-104870 plot burXyl1
076 2010 caeAng1 GCA_000165025.1 Velvet v. 0.7.56 414 41 16726 2 1802 46, 2, scafRNAPATH105:2285-2378 plot caeAng1
077 2012 caeAng2 tbd tbd 461 46 19505 2 1495 46, 2, Cang_2012_03_13_00008:384957-385050 plot caeAng2
078 2008 caeJap1 tbd tbd 135 58 10431 186 27893 687, 10, chrUn:37794313-37795696 plot caeJap1
079 2009 caeJap2 tbd tbd 765 103 130030 1018 891958 707, 10, chrUn:150512438-150513861 plot caeJap2
080 1880 caeJap2a tbd tbd 764 103 129273 1018 890958 707, 10, Cjap_Contig4853:3969-5392 plot caeJap2a
082 2010 caeJap4 GCA_000147155.1 Celera assembler v. 6.0 16 98.5 3188 20 1468 1000, 20, Scaffold17129:65445-67464 plot caeJap4
083 2007 caePb1 tbd tbd 115 44 9160 164 37674 476, 10, chrUn:52430125-52431086 plot caePb1
084 2008 caePb2 tbd tbd 83 37 3814 222 63681 230, 10, chrUn:74484521-74484990 plot caePb2
085 2010 caePb3 GCA_000143925.2 PCAP v. 9/3/04 89 37 4915 222 74680 230, 10, Scfld02_75:384084-384553 plot caePb3
086 2005 caeRem1 tbd tbd 58 96 10213 133.5 11238 678, 10, SuperCont3:723391-724756 plot caeRem1
087 2006 caeRem2 tbd tbd 58 96 10213 133.5 11238 678, 10, chrUn:13919319-13920684 plot caeRem2
088 2007 caeRem3 tbd tbd 46 50 5760 197.5 14178 460, 10, chrUn:27560772-27561701 plot caeRem3
089 2007 caeRem4 GCF_000149515.1 tbd 46 50 5760 197.5 14178 460, 10, Crem_Contig253:25277-26206 plot caeRem4
090 2010 caeSp111 GCA_000186765.1 Celera assembler v. 6.0 4 194.5 760 20 80 333, 20, Scaffold629:32984714-32985399 plot caeSp111
091 2012 caeSp51 tbd tbd 14 34 730 12.5 894 201, 3, Csp5_scaffold_09411:792-1196 plot caeSp51
092 2010 caeSp71 tbd tbd 535 47 30250 213 312209 162, 20, Scaffold11:29462-29805 plot caeSp71
093 2010 caeSp91 tbd tbd 26 217.5 7172 8745 180575 1000, 20, Scaffold7498:303469-305488 plot caeSp91
094 2014 calAnn1 GCF_000699085.1 SOAPdenovo v. 1.6 89 127 16337 1006 168943 440, 38, KL218155:301090-302007 plot calAnn1
095 2007 calJac1 tbd tbd 1597 42 129367 182 377725 937, 10, Contig4771:110891-112774 plot calJac1
096 2009 calJac3 GCF_000004665.1 PCAP v. 2009 1516 43 116646 183.5 452860 807, 10, chr3:111956760-111958383 plot calJac3
097 2013 calMil1 GCF_000165045.1 Celera v. 6.1 31 123 8335 100 70257 1000, 100, KI635945:3331497-3333596 plot calMil1
098 2011 camFer1 GCF_000311805.1 SOAPdenovo v. V1.05 11 205 2059 129 2031 237, 2, KB018701:319294-319769 plot camFer1
099 2004 canFam1 tbd tbd 12 153 2669 210.5 8118 104, 1, chr18:45376349-45376557 plot canFam1
100 2005 canFam2 tbd tbd 32 199.5 8095 1 5245 746, 1, chrUn:76334072-76335564 plot canFam2
101 2011 canFam3 GCF_000002285.3 Arachne v. April 2010 34 175.5 8234 10 4545 746, 10, chrUn_JH374132:3424-4925 plot canFam3
104 2014 capCar1 GCF_000700745.1 SOAPdenovo v. 1.6 4 105 618 48 354 139, 26, KL359104:23556-23859 plot capCar1
105 2012 capHir1 GCF_000317765.1 SOAPdenovo v. 1.03 627 41 71810 100 546475 988, 16, chr16:40339512-40341503 plot capHir1
106 2014 carCri1 GCF_000690535.1 SOAPdenovo v. 1.6 4 161 644 210.5 878 52, 13, KK509558:67998-68114 plot carCri1
107 2017 casCan1 GCF_001984765.1 ABySS v. 1.9.0; Canu v. 1.2; Platanus v. 1.2.4 19 90 2464 100 1900 952, 100, NW_017870822v1:53223-55226 plot casCan1
108 2014 cavApe1 tbd tbd 551 47 32236 24 184424 82, 1, AVPZ01000046v1:610580-610744 plot cavApe1
109 2005 cavPor2 tbd tbd 393 427 164744 100 166667 986, 100, scaffold_291164:123135-125206 plot cavPor2
110 2008 cavPor3 GCF_000151735.1 unknown v. before 2008 3 145 552 100 961 313, 100, scaffold_799:9280-10005 plot cavPor3
111 2002 cb1 tbd tbd 81 163 20408 145 39126 645, 10, chrUn:51532611-51533910 plot cb1
112 2005 cb2 tbd tbd 86 153 21033 163.5 42461 645, 10, chrI:9244132-9245431 plot cb2
113 2007 cb3 tbd tbd 80 148.5 19176 166.5 39580 645, 10, chrI:9355978-9357277 plot cb3
114 2011 cb4 tbd tbd 86 153 20969 151.5 40114 645, 10, chrI:11247250-11248549 plot cb4
125 2016 cebCap1 GCF_001604975.1 AllPaths-LG v. October 2015 1519 64 128197 1 415272 1000, 1, NW_016107342v1:6176614-6178614 plot cebCap1
126 2015 cerAty1 GCF_000955945.1 AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9 433 92 41269 50 137883 865, 25, NW_012007258v1:11321204-11322958 plot cerAty1
127 2012 cerSim1 GCF_000283155.1 ALLPATHS v. R41370 1818 68 129697 100 270005 815, 100, JH767775:6384924-6386653 plot cerSim1
128 2014 chaVoc1 GCF_000708025.1 SOAPdenovo v. 1.6 47 200 13700 1514 133699 780, 257, KL409415:13594818-13596634 plot chaVoc1
129 2014 chaVoc2 GCF_000708025.1 SOAPdenovo v. 1.6 47 200 13700 1514 133699 780, 257, KL873469:13594818-13596634 plot chaVoc2
130 2013 cheMyd1 GCF_000344595.1 SOAPdenovo v. 1.05 129 204 37111 798 277853 314, 27, KB535131:1778822-1779476 plot cheMyd1
131 2012 chiLan1 GCA_000276665.1 ALLPATHS v. R40776 1183 70 101029 100 267937 996, 100, JH721987:2542897-2544988 plot chiLan1
132 2013 chlSab1 tbd tbd 23634 81 2123928 10 396229 923, 1, chrX:117110178-117112024 plot chlSab1
133 2014 chlSab2 GCF_000409795.2 ALLPATHS and Newbler v. 13-Feb-2013 23631 81 2123656 10 396199 923, 1, chrX:117110178-117112024 plot chlSab2
134 2014 chlUnd1 GCF_000695195.1 SOAPdenovo v. 1.6 5 293 1223 129 617 310, 65, KK747264:28313-28997 plot chlUnd1
135 2008 choHof1 GCA_000164785.1 tbd 104 54.5 14520 145.5 33892 986, 100, scaffold_56240:3133-5204 plot choHof1
136 2012 chrAsi1 GCF_000296735.1 allpaths v. R42316 HAPLOIDIFY=True 3416 76 339291 100 720504 991, 100, JH823765:402000-404081 plot chrAsi1
137 2011 chrPic1 tbd tbd 7555 79 738667 50 1230115 64, 1, JH584466:5301285-5301413 plot chrPic1
138 2014 chrPic2 GCA_000241765.2 Newbler v. 2.6 6315 77 629230 206 2593694 1000, 10, chrUn_KK083066v1:1300793-1302802 plot chrPic2
139 2002 ci1 GCA_000183065.1 tbd 28 311.5 8955 50 11060 833, 50, Scaffold_7:289989-291704 plot ci1
140 2005 ci2 tbd tbd 2 472.5 945 173 346 843, 296, scaffold_403:40134-42115 plot ci2
141 2011 ci3 GCF_000224145.1 tbd 22 258.5 6455 50 9493 597, 50, chrUn_NW_004190451v1:5050-6293 plot ci3
142 2003 cioSav1 tbd tbd 8 124 1554 100 2755 296, 100, ps_146:263977-264668 plot cioSav1
143 2005 cioSav2 tbd tbd 6 402.5 2394 200 1668 636, 10, reftig_72:2536022-2537303 plot cioSav2
144 2015 colAng1 GCF_000951035.1 AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2 5690 77 626146 50 1472786 996, 50, NW_012119888v1:35718-37759 plot colAng1
145 2013 colLiv1 GCF_000337935.1 SOAPdenovo v. 2.0 19 116 3824 1290 32865 33, 57, KB379196:2050-2172 plot colLiv1
146 2014 colStr1 GCF_000690715.1 SOAPdenovo v. 1.6 5 161 910 308 1203 362, 113, KK530485:3407-4243 plot colStr1
147 2012 conCri1 GCF_000260355.1 AllPaths v. 2012 1110 72 108033 100 233431 924, 100, JH655880:49229854-49231801 plot conCri1
148 2014 corBra1 GCF_000691975.1 SOAPdenovo v. 1.6 41 90 7520 1445 112176 259, 28, KK718436:193091-193636 plot corBra1
149 2014 corCor1 GCF_000738735.1 AllPaths v. Allpaths-LG version 41687 21 81 2189 1027 27602 81, 1, KL997637:955359-955521 plot corCor1
150 2013 cotJap1 GCA_000511605.1 Soapdenovo v. 1.0.5b; bwa v. 0.5.9; SSPACE v. 1.2 1122 33 38101 68 67651 214, 1, DF262918:84572-85000 plot cotJap1
151 2016 cotJap2 GCF_001577835.1 ALLPATHS-LG v. 4.7.0 628 81 49843 1 166844 808, 1, chr2:125266985-125268601 plot cotJap2
152 2013 criGri1 GCF_000419365.1 SOAPdenovo v. 2.2 588 217 196516 1481.5 1359815 422, 10, KE379019:554914-555767 plot criGri1
153 2011 criGriChoV1 GCF_000223135.1 SOAPdenovo v. 1.05 213 162 53736 1526 472877 369, 10, NW_003615838v1:158557-159304 plot criGriChoV1
154 2017 criGriChoV2 tbd tbd 9581 199 1595358 100 961598 293, 30, LT883673v1:24540519-24541134 plot criGriChoV2
155 2014 cucCan1 GCF_000709325.1 SOAPdenovo v. 1.6 113 242 41656 972 203191 961, 69, KL448150:311854-313844 plot cucCan1
156 2014 cynSem1 GCF_000523025.1 SOAPdenovo v. April-2011 78 311.5 27891 935.5 165198 568, 38, chr11:13981930-13983103 plot cynSem1
157 2014 cypVar1 GCA_000732505.1 AllPaths v. May 2014 3240 89 423504 1 2210432 1000, 1, KL653732:89449-91449 plot cypVar1
158 2003 danRer1 tbd tbd 1280 57 186413 10 322061 1000, 10, chr25:16217228-16219237 plot danRer1
159 2014 danRer10 GCF_000002035.5 tbd 575 174 105525 10 17550 484, 10, chr5:1032421-1033398 plot danRer10
160 2017 danRer11 GCF_000002035.6 tbd 127 124 25120 100 12650 42, 1, chr16:27147800-27147884 plot danRer11
161 2004 danRer2 tbd tbd 1150 58 191859 10 223764 1000, 10, chr10:26174984-26176993 plot danRer2
162 2005 danRer3 tbd tbd 819 58 88143 10 121196 776, 10, chrUn:112388525-112390086 plot danRer3
163 2006 danRer4 tbd tbd 726 65.5 121967 14 135012 705, 11, chr25:30060270-30061690 plot danRer4
164 2007 danRer5 tbd tbd 1559 170 288298 100 155702 73, 1, chr21:35548773-35548919 plot danRer5
165 2008 danRer6 tbd tbd 1421 133 225674 100 142101 1000, 100, Zv8_scaffold431:54613-56712 plot danRer6
166 2010 danRer7 GCF_000002035.4 tbd 1245 164 217595 100 124500 900, 100, chr22:2241720-2243619 plot danRer7
167 2005 dasNov1 tbd tbd 55 123 12971 111 31368 681, 100, scaffold_3005:3743-5204 plot dasNov1
168 2008 dasNov2 tbd tbd 109 136 25865 100 58752 836, 100, scaffold_3394:70496-72267 plot dasNov2
169 2011 dasNov3 GCF_000208655.1 Celera Assembler v. 6.0; Atlas-Link; Atlas-Gap-Fill 239 46 16270 50 94236 677, 50, JH564516:24848-26251 plot dasNov3
170 2014 dicLab1 GCA_000689215.1 tbd 275 423 116519 203 134149 994, 20, HG916850:2956140-2958147 plot dicLab1
171 2008 dipOrd1 GCA_000151885.1 tbd 219 46 46012 379 102683 1000, 100, scaffold_2463:9467-11566 plot dipOrd1
172 2014 dipOrd2 GCF_000151885.1 AllPaths LG v. 41070; Atlas Link v. 2.0; Atlas GapFill v. 2.0 3290 64.5 258868 50 821432 981, 50, NW_012267268v1:6944272-6946283 plot dipOrd2
173 2013 dirImm1 tbd tbd 505 175 132528 2 32073 999, 1, nDi_2_2_scaf00035:47420-49418 plot dirImm1
174 2003 dm1 tbd tbd 9 252 2984 20 1237 604, 20, chrU:5250525-5251752 plot dm1
175 2004 dm2 tbd tbd 8 362 2818 20 1217 604, 20, chrU:5250525-5251752 plot dm2
176 2006 dm3 tbd tbd 20 286 4907 100 423940 276, 20, chrU:4943122-4943693 plot dm3
177 2014 dm6 GCF_000001215.4 tbd 15 333 4828 100 1340 276, 20, chrUn_DS483709v1:12934-13505 plot dm6
178 2003 dp2 tbd tbd 113 64 11633 10 9049 784, 10, Contig4969_Contig4496:202614-204191 plot dp2
179 2004 dp3 tbd tbd 136 79.5 17354 79.5 14988 485, 11, chrU:7044759-7045739 plot dp3
180 2006 dp4 tbd tbd 183 81 19720 50 18528 798, 50, chrXL_group1e:8376310-8377955 plot dp4
181 2012 droAlb1 GCA_000298335.1 SOAPdenovo v. 1.04 4360 30 131320 22 152454 76, 1, JH853217:889-1041 plot droAlb1
182 2004 droAna1 tbd tbd 103 252 28853 100 10300 943, 100, 2448822:95133-97118 plot droAna1
183 2005 droAna2 tbd tbd 32 160 7905 701 72786 791, 25, scaffold_13266:420335-421941 plot droAna2
184 2006 droAna3 GCF_000005115.1 tbd 35 143 8663 671 75001 707, 25, scaffold_13230:483470-484908 plot droAna3
185 2013 droBia2 GCA_000233415.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 14 116.5 2103 20 294 447, 20, KB462730:148150-149063 plot droBia2
186 2013 droBip2 GCA_000236285.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_calland_upgrade.pl v. 1.0 26 103.5 3925 20 520 409, 20, KB464242:790791-791628 plot droBip2
187 2013 droEle2 GCA_000224195.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATKv. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 22 205 4879 20 440 480, 20, KB458480:1051747-1052726 plot droEle2
188 2005 droEre1 tbd tbd 8 86.5 1545 731 6855 773, 25, scaffold_4784:23686196-23687766 plot droEre1
189 2006 droEre2 GCF_000005135.1 tbd 14 221 4384 239 7433 763, 25, scaffold_4784:18133045-18134595 plot droEre2
190 2013 droEug2 GCA_000236325.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 17 52 1627 20 237 72, 1, AFPQ02002129:815-959 plot droEug2
191 2013 droFic2 GCA_000220665.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 11 352 3277 20 220 424, 20, KB457328:1582-2449 plot droFic2
192 2005 droGri1 tbd tbd 17 76 2908 444 11143 734, 312, scaffold_24659:1579-3358 plot droGri1
193 2006 droGri2 GCF_000005155.2 tbd 48 60.5 5904 430.5 52107 774, 25, scaffold_15245:16809148-16810720 plot droGri2
194 2013 droKik2 GCA_000224215.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 12 102 1812 20 1721 361, 20, KB458730:24774-25515 plot droKik2
195 2013 droMir2 GCA_000269505.2 Newbler v. 2.6 122 72 16465 10 57520 1000, 10, chr2:9770771-9772780 plot droMir2
197 2005 droMoj2 tbd tbd 22 219.5 7748 366.5 30847 969, 25, scaffold_6496:4573125-4575087 plot droMoj2
198 2006 droMoj3 GCF_000005175.2 tbd 16 343 6118 426 29359 859, 25, scaffold_6496:14181729-14183471 plot droMoj3
199 2005 droPer1 GCF_000005195.2 tbd 28 402 10502 100 10914 937, 100, super_12:105769-107742 plot droPer1
200 2013 droPse3 GCF_000001765.3 PBJelly v. 12.8.2; Atlas genome assembly 12 51 1309 86 3307 718, 50, chr3:13529933-13531418 plot droPse3
201 2013 droRho2 GCA_000236305.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 35 167 7228 20 1286 454, 20, KB451407:7018-7945 plot droRho2
202 2005 droSec1 GCA_000005215.1 tbd 17 399 6822 100 5318 765, 100, super_59:77146-78775 plot droSec1
203 2005 droSim1 tbd tbd 109 106 23001 298 40703 801, 10, chr2L:4623692-4625303 plot droSim1
204 2014 droSim2 GCF_000754195.2 Velvet v. 1.1.04 104 58 5999 10 1818 359, 8, chr2R:7425888-7426613 plot droSim2
205 2013 droSuz1 GCA_000472105.1 SOAPdenovo v. 2 71 185 16489 1565 196054 364, 76, KI420423:11753-12556 plot droSuz1
206 2013 droTak2 GCA_000224235.2 Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0 13 102 2070 20 260 472, 20, KB461286:709634-710597 plot droTak2
207 2004 droVir1 tbd tbd 48 328.5 15839 25 16648 698, 25, scaffold_10:2740496-2741916 plot droVir1
208 2005 droVir2 tbd tbd 13 232 3421 1415 46365 503, 25, scaffold_13324:149342-150372 plot droVir2
209 2006 droVir3 GCF_000005245.1 tbd 12 341 4206 1536.5 45200 423, 25, scaffold_13324:149231-150101 plot droVir3
210 2006 droWil1 GCF_000005925.1 tbd 23 248 8712 1330 51159 759, 50, scaffold_181150:697726-699293 plot droWil1
211 2006 droWil2 GCF_000005925.1 tbd 23 248 8712 1330 51159 759, 50, CH964291:697726-699293 plot droWil2
212 2004 droYak1 tbd tbd 65 340 25549 250 24358 955, 50, chrU:40768288-40770247 plot droYak1
213 2005 droYak2 tbd tbd 99 170 26922 54 37713 684, 10, chr2L:22155365-22156742 plot droYak2
214 2006 droYak3 GCF_000005975.2 tbd 85 143 20479 10 23713 684, 10, chr2L:22155365-22156742 plot droYak3
217 2005 echTel1 tbd tbd 89 83 17114 100 22024 805, 100, scaffold_272928:13200-14909 plot echTel1
218 2012 echTel2 GCF_000313985.1 ALLPATHS v. R37599 3871 93 620444 100 656358 998, 100, JH980317:1376657-1378752 plot echTel2
219 2014 egrGar1 GCF_000687185.1 SOAPdenovo v. 1.6 112 213.5 33121 1093.5 229589 998, 134, KK502338:445846-447975 plot egrGar1
220 2013 eidHel1 GCA_000465285.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 27 45 1294 1 186 68, 1, KE769079:2720-2856 plot eidHel1
221 2012 eleEdw1 GCF_000299155.1 allpaths v. R42301 HAPLOIDIFY=True 1643 71 141553 100 311199 1000, 100, JH947463:2106240-2108339 plot eleEdw1
222 2012 eptFus1 GCF_000308155.1 ALLPATHS v. R40371 1641 75 188916 100 378407 988, 100, JH977647:11513546-11515621 plot eptFus1
223 2007 equCab1 tbd tbd 17 457 5982 100 6200 715, 100, chr2:10720193-10721722 plot equCab1
224 2007 equCab2 tbd tbd 4 160.5 610 1909 18507 258, 295, chr22:17653073-17653883 plot equCab2
225 2018 equCab3 GCF_002863925.1 Celera Assembler v. 2017; HiRise v. 2017 41 666 24283 1000 38458 949, 20, chr10:36118300-36120217 plot equCab3
226 2014 equPrz1 GCA_000696695.1 SOAPdenovo v. 1.05 39 49 5163 49 12408 78, 11, KK955445:38997-39163 plot equPrz1
227 2006 eriEur1 tbd tbd 343 435 146738 100 209198 1000, 100, scaffold_366352:52823-54922 plot eriEur1
228 2012 eriEur2 GCF_000296755.1 allpaths v. R41008 3596 70 265454 100 1205265 1000, 100, JH835375:3514396-3516495 plot eriEur2
229 2014 esoLuc1 GCA_000721915.1 AllPaths v. 43500 9785 81 734131 15 1227519 950, 10, LG19:14032217-14034126 plot esoLuc1
231 2015 eulFla1 tbd tbd 29206 139 4756877 1 60241 986, 1, LGHW01004502v1:47323-49295 plot eulFla1
232 2015 eulMac1 tbd tbd 41489 62 3147719 53 2639442 393, 1, LGHX01000676v1:768695-769481 plot eulMac1
233 2014 eurHel1 GCF_000690775.1 SOAPdenovo v. 1.6 2 89.5 179 436 872 113, 451, KK569808:53808-54484 plot eurHel1
235 2013 falChe1 GCF_000337975.1 SOAPdenovo v. 1.4 27 206 7614 685 35918 51, 10, KB397780:7020361-7020472 plot falChe1
236 2013 falPer1 GCF_000337955.1 SOAPdenovo v. 1.4 6 48.5 530 631.5 4836 36, 10, KB391040:3398436-3398517 plot falPer1
237 1880 felCat1 tbd tbd 1343 353 504058 874 2708782 1000, 100, scaffold_217423:45453-47552 plot felCat1
238 2006 felCat3 tbd tbd 1343 353 504058 874 2708782 1000, 100, scaffold_217423:45453-47552 plot felCat3
239 2008 felCat4 GCA_000003115.1 tbd 9736 503 4582767 10 9398414 1000, 10, chrA2:8725380-8727389 plot felCat4
240 2011 felCat5 GCF_000181335.1 Celera Assembler v. 6.1 27 72 6437 20 100569 488, 20, chrB2:22462351-22463346 plot felCat5
241 2014 felCat8 GCF_000181335.2 CABOG v. 6.2; MaSuRCA assembler v. 8.0; GAA v. 1.0 630 55 50300 10 89447 895, 14, chrB3:27250577-27252380 plot felCat8
243 2013 ficAlb1 GCF_000247815.1 SOAPdenovo v. 1.05 632 77 75592 40.5 206854 982, 1, chr7:28154426-28156390 plot ficAlb1
244 2013 ficAlb2 GCF_000247815.1 SOAPdenovo v. 1.05 632 77 75592 40.5 206854 982, 1, chr7:28154426-28156390 plot ficAlb2
245 2002 fr1 tbd tbd 76 155.5 19306 50 16684 71, 1, chrUn:149577204-149577346 plot fr1
246 2004 fr2 tbd tbd 5 313 1682 512 2231 47, 1, chrUn:336404518-336404612 plot fr2
247 2011 fr3 GCF_000180615.1 tbd 6 229 1827 286 2291 47, 1, HE592038:5063-5157 plot fr3
248 2014 fukDam1 GCF_000743615.1 SOAPdenovo v. 1.06 793 203 238200 519 931836 991, 10, NW_011045963v1:25160-27151 plot fukDam1
249 2014 fulGla1 GCF_000690835.1 SOAPdenovo v. 1.6 8 336.5 2583 103.5 1637 450, 20, KK597768:8602-9521 plot fulGla1
250 2010 gadMor1 GCA_000231765.1 tbd 168 53 11363 270 70748 51, 1, CAEA01526699:46-148 plot gadMor1
251 2004 galGal2 tbd tbd 114 40 12930 124 17674 778, 21, chr3:68417113-68418689 plot galGal2
252 2006 galGal3 tbd tbd 729 37 34199 500 325853 479, 10, chrUn_random:55035794-55036761 plot galGal3
253 2011 galGal4 GCF_000002315.3 Celera Assembler v. 5.4 55 401 22946 100 31537 805, 100, chr19:3903221-3904930 plot galGal4
254 2015 galGal5 GCF_000002315.4 MHAP/PBcR v. 8.2beta 1 33 33 795 795 33, 795, chrUn_NT_465606v1:9086-9946 plot galGal5
256 2014 galVar1 GCF_000696425.1 SOAPdenovo2 v. April 2014 58964 61 5626241 419 24866346 997, 1, NW_007727116v1:311725-313719 plot galVar1
257 2006 gasAcu1 tbd tbd 8 46.5 1970 117.5 2520 841, 100, chrUn:38727446-38729227 plot gasAcu1
259 2009 gavGan0 tbd tbd 30236 134 5187944 5000 145799649 915, 10, scaffold24725:12789-14628 plot gavGan0
260 2014 gavSte1 GCF_000690875.1 SOAPdenovo v. 1.6 5 164 848 318 2312 269, 245, KK640233:828-1610 plot gavSte1
261 2012 geoFor1 GCF_000277835.1 SOAPdenovo v. 2.01 32 105.5 4877 945.5 51025 617, 11, JH739922:1318693-1319937 plot geoFor1
263 2009 gorGor2 tbd tbd 6585 247 2365617 10 499615 1000, 10, chr10_101645027_418909:206049-208058 plot gorGor2
264 2011 gorGor3 GCF_000151905.1 tbd 6926 246 2475426 10 533805 1000, 10, chr10:101539188-101541197 plot gorGor3
265 2014 gorGor4 GCA_000151905.3 tbd 8691 94 1514940 25 982883 246, 1, chr9:24397320-24397812 plot gorGor4
267 2009 haeCon1 tbd tbd 25 39 1031 10 1745 58, 10, Hcon_Contig0056815:13389-13514 plot haeCon1
268 2013 haeCon2 tbd tbd 5378 149 831727 55 351011 700, 1, scaffold_63:260903-262303 plot haeCon2
269 2014 halAlb1 GCF_000691405.1 SOAPdenovo v. 1.6 11 126 1936 370 3807 466, 102, KK641449:26277-27310 plot halAlb1
270 2014 halLeu1 GCF_000737465.1 SOAPdenovo2 v. May 2014 14 280 4342 95 1676 194, 10, KL869356:8708537-8708934 plot halLeu1
271 2011 hapBur1 GCF_000239415.1 ALLPATHS-LG v. R35951 965 95 135908 20 374038 975, 20, JH425754:7557-9526 plot hapBur1
273 2011 hetBac1 GCA_000223415.1 Celera assembler v. 6.0 3 228 1282 20 60 1000, 20, GL996479v1:885362-887381 plot hetBac1
274 2011 hetGla1 tbd tbd 743 313 285174 1994 2914751 785, 43, JH165660:4306-5918 plot hetGla1
275 2012 hetGla2 GCF_000247695.1 AllPaths v. R39605 595 70 44604 100 201552 1000, 100, JH602085:17402968-17405067 plot hetGla2
276 2009 hg19 tbd tbd 1 200 200 3000000 3000000 200, 3000000, chrY:10104354-13104753 plot hg19
277 2013 hg38 GCF_000001405.26 tbd 12 78 974 440 56689 125, 20, chrUn_KI270442v1:175618-175887 plot hg38
281 2012 jacJac1 GCF_000280705.1 ALLPATHS v. R41689 HAPLOIDIFY=True 2666 63 196366 100 569918 1000, 100, JH725440:52488719-52490818 plot jacJac1
282 2011 latCha1 GCF_000225785.1 AllPaths v. R36819 2038 77 159059 100 504858 955, 100, JH127253:476850-478859 plot latCha1
284 2014 lepDis1 GCF_000691785.1 SOAPdenovo v. 1.6 1 50 50 229 229 50, 229, KK681583:9399-9727 plot lepDis1
285 2011 lepOcu1 GCF_000242695.1 AllPaths v. R38293 2079 95 232474 100 466733 1000, 100, chrLG4:37780111-37782210 plot lepOcu1
286 2013 lepWed1 GCF_000349705.1 allpaths v. R41856 HAPLOIDIFY=True 2022 63 135843 100 1218867 1000, 100, KB715312:1023296-1025395 plot lepWed1
287 2013 letCam1 GCA_000466285.1 Newbler v. 2.7 1453 69 123952 100 739039 280, 39, KE994354:70338-70936 plot letCam1
288 1880 linHum0 GCF_000217595.1 CABOG v. 5.3 179 48 10176 100 20986 480, 100, NW_012159984:28893-29952 plot linHum0
289 2013 lipVex1 GCF_000442215.1 SOAPdenovo v. 2.01 292 92 66483 985.5 386576 876, 10, KE557659:158624-160385 plot lipVex1
290 2012 loaLoa1 GCA_000183805.3 Newbler v. 2.1-PreRelease-4/28/2009 376 382 123384 215 94547 604, 20, JH712068v1:803529-804756 plot loaLoa1
291 2005 loxAfr1 tbd tbd 79 44 11426 206 80801 687, 284, scaffold_10531:71539-73196 plot loxAfr1
292 2008 loxAfr2 tbd tbd 78 165.5 20735 1078 180887 989, 100, scaffold_3386:17920-19997 plot loxAfr2
293 2009 loxAfr3 GCF_000001905.1 tbd 11 45 1924 398 9784 731, 100, scaffold_211:333226-334787 plot loxAfr3
294 2007 macEug1 tbd tbd 7319 57 504656 10 562759 146, 1, Scaffold27901:25044-25336 plot macEug1
295 2009 macEug2 GCA_000004035.1 tbd 11689 55 752361 50 1102638 146, 1, GL058785:13153-13445 plot macEug2
296 2013 macFas5 GCF_000364345.1 SOAPdenovo v. 1.0.5, SRPRISM v. 2.4; ARGO v. 0.1 1138 106.5 145024 204.5 1039415 849, 10, chr14:81860376-81862083 plot macFas5
297 2015 macNem1 GCF_000956065.1 AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2; PBJelly2 v. 14.9.9 1828 95 237662 50 834836 982, 25, NW_012016132v1:18826350-18828338 plot macNem1
298 2015 manLeu1 GCF_000951045.1 AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v. 2.2 6092 95 1723434 50 1354856 1000, 50, NW_012101473v1:89787-91836 plot manLeu1
299 2014 manPen1 GCA_000738955.1 SOAPdenovo v. May 2014 37129 101 5536376 1 13090743 1000, 1, KN006700:349054-351054 plot manPen1
300 2014 manVit1 GCF_000692015.1 SOAPdenovo v. 1.6 25 231 8844 1303 65245 701, 296, KK732740:655429-657126 plot manVit1
302 2012 mayZeb1 GCF_000238955.1 AllPaths v. R37043 1831 95 241336 100 682313 1000, 100, JH720538:3252564-3254663 plot mayZeb1
303 2013 megLyr1 GCA_000465345.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 33 38 1716 1 185 83, 1, KI087181:1999-2165 plot megLyr1
304 2009 melGal1 tbd tbd 834 127 136229 100 661041 169, 1, chr3:54352580-54352918 plot melGal1
305 2014 melGal5 GCF_000146605.2 MaSuRCA v. 1.9.2 84 181 17431 100 76065 724, 100, chrZ:7873702-7875249 plot melGal5
308 2008 melInc2 tbd tbd 3 77 211 201 513 98, 201, MiV1ctg3:286050-286446 plot melInc2
309 2011 melUnd1 GCF_000238935.1 Celera v. 6.1 39 89 5925 41 36796 334, 20, JH556232:114057-114744 plot melUnd1
310 2014 merNub1 GCF_000691845.1 SOAPdenovo v. 1.6 2 154.5 309 361 722 245, 311, KK701714:10568-11368 plot merNub1
311 2013 mesAur1 GCF_000349665.1 allpaths v. R44683 3589 71 248381 100 755166 212, 100, KB708269:3930600-3931123 plot mesAur1
312 2014 mesUni1 GCF_000695765.1 SOAPdenovo v. 1.6 4 347 1434 124.5 451 332, 23, KK817080:7082-7768 plot mesUni1
313 1880 micMur0 tbd tbd 295 256 90483 780 749299 997, 100, GeneScaffold_4747:166512-168605 plot micMur0
314 2007 micMur1 GCA_000165445.1 tbd 124 124.5 33320 952.5 207469 969, 100, scaffold_5185:107104-109141 plot micMur1
315 2015 micMur2 GCF_000165445.1 AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9 774 90 85250 50 267164 999, 25, KQ057470v1:2292330-2294352 plot micMur2
316 2017 micMur3 GCF_000165445.2 AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9; Lachesis v. shendurelab-LACHESIS-2151de9; BioNano IrysSolve v. 2.1 325 95 73918 50 262987 898, 10, chr2:108635511-108637316 plot micMur3
317 2012 micOch1 GCF_000317375.1 allpaths v. R41985 HAPLOIDIFY=True SPRS_WRITE_SEPS=True 6788 65 483435 100 1507707 993, 100, chr6:54381083-54383168 plot micOch1
318 2011 mm10 tbd tbd 2 390.5 781 25879.5 51759 477, 1759, chrX_GL456233_random:239940-242652 plot mm10
319 1880 mm5 tbd tbd 204 48.5 30180 100 76884 921, 100, chr6:132460596-132462537 plot mm5
320 2005 mm6 tbd tbd 117 48 17647 100 48212 768, 100, chr14:100566071-100567706 plot mm6
321 2005 mm7 tbd tbd 45 48 5475 100 64491 451, 100, chr15:68974498-68975499 plot mm7
322 2006 mm8 tbd tbd 6 161 1257 162.5 50878 520, 353, chr14:87009574-87010966 plot mm8
323 2007 mm9 tbd tbd 2 390.5 781 25879.5 51759 477, 1759, chrX_random:239940-242652 plot mm9
324 2004 monDom1 tbd tbd 18 53.5 1891 127 11341 696, 100, scaffold_14754:178069-179560 plot monDom1
325 2005 monDom2 tbd tbd 5 428 2012 100 520 870, 100, scaffold_38:23849795-23851634 plot monDom2
326 2006 monDom4 tbd tbd 9 183 3070 1000 21732 870, 1, chr1:400420041-400421781 plot monDom4
327 2006 monDom5 tbd tbd 9 183 3070 1000 21732 870, 1, chr1:424248968-424250708 plot monDom5
328 2013 musDom2 GCF_000371365.1 AllPathsLG v. September 2012 1284 85 165577 1 473996 1000, 1, KB855954:134298-136298 plot musDom2
329 2011 musFur1 GCA_000215625.1 ALLPATHS-LG v. R36167 1009 84 107706 44 286510 1000, 20, GL897138:9717-11736 plot musFur1
330 2013 myoBra1 GCF_000412655.1 SOAP de novo v. 2.04 356 119 85889 1109 766318 1000, 31, KE163605:2655193-2657223 plot myoBra1
331 2012 myoDav1 GCF_000327345.1 SOAPdenovo v. 1.06 303 151 56967 1283 942238 502, 19, KB106370:3092722-3093744 plot myoDav1
332 2006 myoLuc1 tbd tbd 42 47 6392 1551 125787 388, 100, scaffold_150441:136761-137636 plot myoLuc1
333 2010 myoLuc2 GCF_000147115.1 Arachne v. Dev. Jan 2010 7 39 357 410 3363 75, 119, GL429781:8032929-8033197 plot myoLuc2
334 2014 nanGal1 GCF_000622305.1 SOAPdenovo v. 2.04.4 730 126 149781 902.5 980462 740, 12, KL200152:4088120-4089611 plot nanGal1
335 2015 nanPar1 GCA_000935625.1 SOAPdenovo v. 1.06 1716 194 477991 974 2590489 552, 12, KN907832v1:31307-32422 plot nanPar1
336 2014 nasLar1 GCA_000772465.1 phredPhrap v. 1.080812 614 43 93736 7 126885 117, 1, chr1:6190345-6190579 plot nasLar1
337 2013 necAme1 GCF_000507365.1 Newbler v. MapAsmResearch-04/19/2010-patch-08/17/2010 459 54 28538 100 92887 366, 100, KI657476v1:37386-38217 plot necAme1
338 2007 nemVec1 tbd tbd 25 378 10288 829 17106 769, 1, scaffold_3968:6459-7997 plot nemVec1
339 2011 neoBri1 GCF_000239395.1 ALLPATHS-LG v. R36800 5040 95 1321574 20 665865 998, 20, JH422308:3325010-3327025 plot neoBri1
340 2017 neoSch1 GCF_002201575.1 RefAligner v. 5122; Supernova v. 1.1 882 47 69252 100 596284 888, 100, NW_018726759v1:1-1876 plot neoSch1
341 2014 nipNip1 GCF_000708225.1 SOAPdenovo v. 1.6 41 154 11937 1090 77358 514, 15, KL411148:2104426-2105468 plot nipNip1
342 2010 nomLeu1 tbd tbd 859 141 220161 532 1139352 999, 100, GL397299:16863535-16865632 plot nomLeu1
343 2011 nomLeu2 tbd tbd 859 141 220161 532 1139352 999, 100, GL397299:16863535-16865632 plot nomLeu2
344 2012 nomLeu3 GCA_000146795.3 tbd 861 141 220464 519 1139552 999, 100, chr5:41669854-41671951 plot nomLeu3
345 2014 notCor1 GCF_000735185.1 Celera Assembler v. 7.0 174 91.5 17942 51 21717 407, 1, KL665414:596304-597118 plot notCor1
346 1880 ochPri0 tbd tbd 569 101 138948 1065 1840608 994, 100, GeneScaffold_4726:276480-278567 plot ochPri0
347 2008 ochPri2 GCA_000164825.1 tbd 313 55 35317 1365 1110261 967, 100, scaffold_3914:61889-63922 plot ochPri2
348 2012 ochPri3 GCF_000292845.1 Allpaths v. R41206 1958 69 148238 100 499781 890, 100, JH802177:1348834-1350713 plot ochPri3
349 2012 octDeg1 GCF_000260255.1 allpaths v. R40507 LITTLE_HELPS_BIG=False 2582 68 231489 100 464548 985, 100, JH651571:12809669-12811738 plot octDeg1
350 2013 odoRosDiv1 GCA_000321225.1 AllPaths v. 41070; Atlas-link v. 1.0; Atlas-gapfill v. 2.2 2581 68 180258 50 263661 970, 50, KB229427:1083192-1085181 plot odoRosDiv1
351 2013 oncVol1 GCA_000499405.1 tbd 10 89.5 2046 1 18211 739, 1, HG738137v1:12037947-12039425 plot oncVol1
352 2014 opiHoa1 GCF_000692075.1 SOAPdenovo v. 1.6 80 170.5 23360 1723.5 216549 855, 28, KK733898:82987-84724 plot opiHoa1
353 2013 orcOrc1 GCF_000331955.2 AllPaths v. 41070; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2 2677 66 181922 50 357696 943, 50, NW_004438742v1:126518-128453 plot orcOrc1
354 2011 oreNil1 tbd tbd 1903 93 208888 20 734264 969, 20, GL831201:3474999-3476956 plot oreNil1
356 2007 ornAna1 GCF_000002275.2 tbd 793 49 70053 103 148119 718, 10, Contig3645:38619-40064 plot ornAna1
357 2007 ornAna2 GCA_000002275.2 tbd 793 49 70053 103 148119 718, 10, chrUn_DS182721v1:38619-40064 plot ornAna2
358 2012 oryAfe1 GCF_000298275.1 allpaths v. R40776 LITTLE_HELPS_BIG=False 3595 65 293465 100 691489 998, 100, JH863829:9451309-9453404 plot oryAfe1
359 2005 oryCun1 tbd tbd 122 278.5 44566 462.5 91832 978, 100, scaffold_172390:787-2842 plot oryCun1
360 2009 oryCun2 GCF_000003625.3 tbd 12 44.5 836 446 9055 327, 185, chr13:6520795-6521633 plot oryCun2
361 2006 oryLat1 tbd tbd 141 144 25310 10 215389 561, 10, chrUn:20300712-20301843 plot oryLat1
362 2005 oryLat2 tbd tbd 141 144 25310 10 253399 445, 10, ultracontig221:437957-438856 plot oryLat2
364 2011 otoGar3 GCF_000181295.1 ALLPATHS-LG v. R35710 3569 86 332700 39 663694 985, 20, GL873641:2218538-2220527 plot otoGar3
365 2010 oviAri1 GCA_000005525.1 tbd 5934 53 394316 37 1966190 264, 1, chr15:8985870-8986398 plot oviAri1
366 2012 oviAri3 GCF_000298735.1 SOAPdenovo v. 1.03 149 193 51933 215 178445 46, 3, chr3:3466521-3466615 plot oviAri3
367 2015 oviAri4 GCF_000298735.2 SOAPdenovo v. 1.03; PBJelly2 v. 14.9.9 123 285 48608 100 99192 46, 3, chr3:3435119-3435213 plot oviAri4
368 2015 oxyTri2 tbd tbd 523 37 30028 50 25856 186, 1, chrMACsb310:15510646-15511018 plot oxyTri2
369 2013 panHod1 GCF_000400835.1 SOAPdenovo v. 2.1 321 129 65178 1092 702884 628, 10, KE118776:1218541-1219806 plot panHod1
370 2012 panPan1 GCF_000258655.1 Celera Assembler v. 5.4.3 63 133 11209 20 22114 33, 1, JH650468:842203-842269 plot panPan1
371 2015 panPan2 tbd tbd 70 160 13388 20 1045522 35, 1, chr4:127787143-127787213 plot panPan2
372 2013 panRed1 GCA_000341325.1 Velvet v. 1.2.07 123 56 6626 10 3069 62, 10, KB454926:42673-42806 plot panRed1
373 2013 panTig1 GCF_000464555.1 SOAPdenovo v. 08-Jul-2011 59 111 12591 700 69429 398, 9, KE721804:6447970-6448774 plot panTig1
374 2003 panTro1 tbd tbd 5719 388 2244063 100 3504041 998, 100, chr6:137473031-137475126 plot panTro1
375 2006 panTro2 tbd tbd 692 52 62006 240 238273 717, 10, chr10_random:5205395-5206838 plot panTro2
376 2010 panTro3 tbd tbd 472 54 44241 238.5 180280 908, 10, chr2B:124438762-124440587 plot panTro3
377 2011 panTro4 GCF_000001515.6 tbd 472 54 44241 238.5 180280 908, 10, chr2B:124438762-124440587 plot panTro4
378 2016 panTro5 GCF_000001515.7 DiscoVar v. 51280; PBJelly v. 14.9.9 2937 199 537385 100 3625772 199, 10, chr12_NW_015974005v1_random:1130-1537 plot panTro5
379 2018 panTro6 GCF_002880755.1 tbd 5 667 3499 100 18496 1000, 100, chr8:127452460-127454559 plot panTro6
380 2012 papAnu2 GCF_000264685.1 CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0 727 138 144060 50 96682 46, 1, chr4:20965571-20965663 plot papAnu2
381 2013 papAnu3 GCF_000264685.2 CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0 727 138 144060 50 96682 46, 1, chr4:20965571-20965663 plot papAnu3
382 2017 papAnu4 GCF_000264685.3 CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0; PBJelly2 v. 14.9.9; Pilon v. 1.18 368 238.5 95783 50 84582 703, 10, chrUn_NW_018824177v1:2651-4066 plot papAnu4
383 2008 papHam1 tbd tbd 22041 56 1338445 50 2303596 376, 50, scaffold4259:86690-87491 plot papHam1
384 2014 pelCri1 GCF_000687375.1 SOAPdenovo v. 1.6 3 72 517 186 808 386, 173, KK471910:16412-17356 plot pelCri1
385 2011 pelSin1 GCF_000230535.1 SOAPdenovo v. 1.05 126 138 35062 411.5 167243 398, 10, JH212629:287260-288065 plot pelSin1
386 2013 perManBai1 GCF_000500345.1 Newbler v. 2.3 and 2.5; AllPaths v. 41070; ATLAS-gapfill v. 2.2; ATLAS-link v. 1.0 7908 80 846184 50 1552640 1000, 50, KI615759:2266069-2268118 plot perManBai1
387 2007 petMar1 tbd tbd 542 47 48234 10 42185 746, 10, Contig3178:18125-19626 plot petMar1
388 2010 petMar2 GCA_000148955.1 Arachne v. 3.2 31 86 5681 732 39461 617, 100, GL479790:15647-16980 plot petMar2
389 2017 petMar3 tbd tbd 40 242.5 11527 100 119063 718, 1, PIZI01000010v1:16691860-16693296 plot petMar3
390 2014 phaCar1 GCF_000708925.1 SOAPdenovo v. 1.6 2 206 412 79 158 261, 100, KL416242:66648-67269 plot phaCar1
391 2014 phaLep1 GCF_000687285.1 SOAPdenovo v. 1.6 14 179 2930 310 4227 343, 85, KK448216:3226-3996 plot phaLep1
392 2014 phoRub1 GCA_000687265.1 SOAPdenovo v. 1.6 4 288.5 1016 195.5 823 373, 83, KK425162:48893-49721 plot phoRub1
393 2013 phyCat1 GCF_000472045.1 AllPaths-LG v. January 2013 684 82.5 86555 100 130377 1000, 1, KI402232:538054-540054 plot phyCat1
394 2014 picPub1 GCF_000699005.1 SOAPdenovo v. 1.6 59 83 12175 970 106482 111, 28, KL217012:74310-74559 plot picPub1
395 2013 poeFor1 GCF_000485575.1 AllPaths-LG v. July 2013 848 75 84492 1 328834 972, 1, KI520524:847-2791 plot poeFor1
396 2014 poeRet1 tbd tbd 1124 87 157426 1 421252 988, 1, chrLG12:26078504-26080480 plot poeRet1
397 1880 ponAbe1 tbd tbd 1528 40 90824 133.5 275853 662, 10, Contig208:1185633-1186966 plot ponAbe1
398 2007 ponAbe2 tbd tbd 2239 54 444541 100 829820 769, 1, chr11:46659515-46661053 plot ponAbe2
400 2014 priExs1 tbd tbd 49 121 12100 1773 95166 181, 38, scaffold470:42605-43004 plot priExs1
401 2007 priPac1 tbd tbd 121 49 10688 209 31254 90, 1, chrUn:114913780-114913960 plot priPac1
403 2014 priPac3 tbd tbd 168 49.5 13153 274.5 50322 90, 1, Ppa_Contig2432:805-985 plot priPac3
404 2008 proCap1 GCA_000152225.1 Arachne v. before 2009 116 38 5205 534.5 65619 53, 100, scaffold_8867:32393-32598 plot proCap1
405 2015 proCoq1 GCF_000956105.1 AllPathsLG v. R43839; Atlas Link v. 1.0; Atlas Gapfill v. 2.2 1491 92 191552 50 427249 970, 50, NW_012149019v1:36737-38726 plot proCoq1
406 2013 pseHum1 GCF_000331425.1 SOAPdenovo v. 1.5 775 142 173055 10 547111 1000, 10, KB221227:5459003-5461012 plot pseHum1
407 2012 pteAle1 GCA_000325575.1 SOAPdenovo v. 1.06 97 127 19728 1023 161616 421, 16, KB031157:14150143-14151000 plot pteAle1
408 2014 pteGut1 GCF_000699245.1 SOAPdenovo v. 1.6 1 282 282 720 720 282, 720, KL237369:530-1813 plot pteGut1
409 2013 ptePar1 GCA_000465405.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 3 31 102 1 3 40, 1, KE827285:1815-1895 plot ptePar1
410 2008 pteVam1 GCA_000151845.1 tbd 68 43.5 9173 301.5 27212 971, 100, scaffold_4327:120126-122167 plot pteVam1
411 2011 punNye1 GCF_000239375.1 ALLPATHS-LG v. R37016 1574 95 242736 20 332782 992, 20, JH419321:67178-69181 plot punNye1
412 2014 pygAde1 GCA_000699105.1 SOAPdenovo v. 1.6 42 113 7740 1160.5 93198 78, 17, KL224983:2418932-2419104 plot pygAde1
413 2013 pytBiv1 GCF_000186305.1 Soap deNovo v. March 2012 21222 101 2315791 99 2845128 649, 10, KE957835:3697-5004 plot pytBiv1
418 2005 rheMac1 tbd tbd 2816 39 116369 50 214725 205, 50, SCAFFOLD120616:17732-18191 plot rheMac1
419 2010 rheMac3 GCA_000230795.1 SOAPdenovo v. 1.0 288 192.5 71777 1140.5 887215 949, 27, chr15:33329332-33331256 plot rheMac3
420 2015 rheMac8 GCF_000772875.2 MaSuRCA v. 1.8.3; PBJelly2 v. 14.9.9 80 99.5 20122 917 437685 823, 20, chr7:1436259-1437924 plot rheMac8
421 2016 rhiBie1 GCF_001698545.1 Newbler v. 71; Anytag v. 70; GOBOND v. 69; GapCloser v. 1.12 4262 228 1007049 1 2148972 965, 1, NW_016817388v1:689035-690965 plot rhiBie1
422 2013 rhiFer1 GCA_000465495.1 CLC NGS Cell v. 3.20.50819; SOAPdenovo v. 1.05 2 42.5 85 1 2 45, 1, KI143993:8550-8640 plot rhiFer1
423 2014 rhiRox1 GCF_000769185.1 SOAPdenovo v. 2013.04 187 158 50999 529 184770 584, 11, KN296100v1:378785-379963 plot rhiRox1
424 1880 ricCom1 GCF_000151685.1 tbd 41 332 13808 738 38675 787, 3, EQ973819:99412-100988 plot ricCom1
425 2003 rn3 tbd tbd 574 143 146802 50 425043 72, 1, chr4:1247786-1247930 plot rn3
426 2004 rn4 tbd tbd 567 141 142452 50 424693 72, 1, chr4:1247786-1247930 plot rn4
427 2012 rn5 tbd tbd 64 516 32231 50 28921 712, 1, chr3:45275318-45276742 plot rn5
428 2014 rn6 GCF_000001895.5 Atlas Assembly suite v. 2.0; CLCbio v. 1.0; Velvet v. 1.0; PBjelly v. 2.0 719 290 280406 50 1258566 712, 1, chr3:40184108-40185532 plot rn6
433 2011 saiBol1 GCA_000235385.1 AllPaths v. R37830 1541 77 139356 100 303093 1000, 100, JH378136:528784-530883 plot saiBol1
435 2011 sarHar1 GCF_000189315.1 Phusion2 v. 1.0 17494 220 2993318 158 6574378 958, 10, chr1_GL834475_random:882665-884590 plot sarHar1
436 2013 sebNig1 GCA_000475235.1 tbd 168 55.5 11782 54.5 11235 82, 2, KI499294:4621-4786 plot sebNig1
437 2013 sebRub1 GCA_000475215.1 SOAPdenovo v. 1.05 119 55 9711 51 8253 142, 1, KI444651:3586-3870 plot sebRub1
438 2014 serCan1 GCF_000534875.1 tbd 213 97 36640 20 33876 971, 1, HG009242:4536330-4538272 plot serCan1
439 2006 sorAra1 tbd tbd 229 330 79670 100 75086 895, 100, scaffold_247593:25660-27549 plot sorAra1
440 2008 sorAra2 GCF_000181275.1 Allpaths v. R41070 3389 75 359891 100 822102 992, 100, JH798160:15867029-15869112 plot sorAra2
441 2008 speTri1 tbd tbd 99 46 12167 879 197520 835, 100, scaffold_1259:158788-160557 plot speTri1
442 2011 speTri2 GCF_000236235.1 ALLPATHS v. R37591 2964 95 353556 100 565083 1000, 100, JH393486:3045059-3047158 plot speTri2
444 2014 stePar1 GCF_000690725.1 ALLPATHS-LG v. August 2013 554 65 47063 1 120402 952, 1, KK580894:321554-323458 plot stePar1
445 1880 strCam0 tbd tbd 20 243 7267 836.5 40260 184, 13, superscaffold45:7169362-7169742 plot strCam0
446 2014 strCam1 GCF_000698965.1 SOAPdenovo v. 1.6 19 246 7125 759 39346 184, 13, KL206666:4120006-4120386 plot strCam1
447 2005 strPur1 tbd tbd 1291 153 303896 50 238579 89, 1, Scaffold16400:576-754 plot strPur1
448 2006 strPur2 tbd tbd 367 55 25281 50 79238 35, 1, Scaffold12735:108654-108724 plot strPur2
449 2009 strPur3 tbd tbd 989 56 64991 96 187408 35, 1, Scaffold740:110486-110556 plot strPur3
450 2011 strPur4 GCF_000002235.3 Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement 1612 100 326953 50 206009 425, 3, Scaffold112:361603-362455 plot strPur4
452 2014 strRat2 GCA_001040885.1 tbd 2 54.5 109 6 12 67, 1, chrUn_LN609483v1:243-377 plot strRat2
454 2009 susScr1 tbd tbd 371 43 34151 100 66500 986, 100, chr2:139016697-139018768 plot susScr1
455 2017 susScr11 GCF_000003025.6 Falcon v. OCT-2015 2 104.5 209 100 200 110, 100, chrY:6779476-6779795 plot susScr11
456 2009 susScr2 tbd tbd 371 43 34151 100 66500 986, 100, chr2:139016697-139018768 plot susScr2
457 1880 taeGut0 tbd tbd 212 45 20495 442 116920 624, 10, Contig233:50949-52206 plot taeGut0
458 2008 taeGut1 tbd tbd 223 45 22373 100 22300 689, 100, chr21_random:54357-55834 plot taeGut1
459 2013 taeGut2 GCF_000151805.1 PCAP v. 2008 219 44 21273 100 21900 624, 100, chr27:56676-58023 plot taeGut2
461 2013 takFla1 GCA_000400755.1 HAPs v. 0.2.2 365 241 91817 788 407496 503, 1, KE121297:329-1335 plot takFla1
462 2013 tarIhg38 tbd tbd 12 78 974 440 56689 125, 20, chrUn_KI270442v1:175618-175887 plot tarIhg38
463 2008 tarSyr1 tbd tbd 331 70 45530 191 102767 892, 100, scaffold_111889:3660-5543 plot tarSyr1
464 2013 tarSyr2 GCF_000164805.1 Celera v. DEC-2012 189 56 17645 20 9572 1000, 20, KE939253v1:939796-941815 plot tarSyr2
465 2014 tauEry1 GCF_000709365.1 SOAPdenovo v. 1.6 1 50 50 394 394 50, 394, KL466072:20829-21322 plot tauEry1
466 2004 tetNig1 tbd tbd 64 272.5 21868 1000 53904 336, 59, chr5:807217-807947 plot tetNig1
467 2007 tetNig2 tbd tbd 70 298 25569 500 32404 336, 59, chr5:799217-799947 plot tetNig2
468 2015 thaSir1 GCF_001077635.1 ALLPATHS-LG v. May 2015 3234 95 407625 666 2420576 981, 1, NW_013657934v1:351094-353056 plot thaSir1
469 2014 tinGut1 GCF_000705375.1 SOAPdenovo v. 1.6 18 96 3855 1086 21982 519, 68, KL400865:236113-237218 plot tinGut1
470 2014 tinGut2 GCF_000705375.1 SOAPdenovo v. 1.6 18 96 3855 1086 21982 519, 68, KL895544:236113-237218 plot tinGut2
471 2005 triCas1 tbd tbd 75 100 8201 50 6900 214, 50, Contig5855_Contig1469:226794-227271 plot triCas1
472 2005 triCas2 tbd tbd 63 62 5442 50 313244 412, 50, chrUn_46:283716-284589 plot triCas2
473 2011 triMan1 GCF_000243295.1 AllPaths v. R38542 5748 75 527972 100 726640 1000, 100, JH594622:8537918-8540017 plot triMan1
474 2011 triSpi1 GCF_000181795.1 PCAP v. January 12, 2007 3 55 806 10 230 705, 10, GL622790v1:172202-173621 plot triSpi1
475 2014 triSui1 GCA_000701005.1 SOAPdenovo v. 2 37 138 7959 1449 82883 120, 68, KL363219v1:83933-84240 plot triSui1
477 2013 tupChi1 GCF_000334495.1 SOAPdenovo v. 1.05 914 220.5 290632 987.5 1823897 861, 16, KB320907:3306581-3308318 plot tupChi1
478 2008 turTru1 tbd tbd 112 41.5 15556 388 52461 993, 100, scaffold_108458:6669-8754 plot turTru1
479 2011 turTru2 GCF_000151865.2 Atlas, Atlas-Link, Atlas-GapFill v. June 2011 5612 70 466776 188.5 1979352 44, 1, JH496197:2095-2183 plot turTru2
480 2014 tytAlb1 GCF_000687205.1 SOAPdenovo v. 1.6 2 170 340 326 652 289, 220, KK379918:2163-2960 plot tytAlb1
481 2014 ursMar1 GCF_000687225.1 SOAPdenovo v. 1.05 205 41 12130 3384 708704 711, 49, KK498595:3401141-3402611 plot ursMar1
482 2007 venter1 tbd tbd 64 411.5 26995 100 64592 862, 20, chr2:102870978-102872721 plot venter1
483 2008 vicPac1 tbd tbd 221 251 71912 276 310711 993, 100, scaffold_812:411693-413778 plot vicPac1
484 2013 vicPac2 GCF_000164845.1 Newbler v. May-2012 1245 69 115488 369 430947 685, 20, KB632527:971889-973278 plot vicPac2
485 1880 vicVic1 tbd tbd 218 252.5 71401 263 309237 993, 100, scaffold_812:411693-413778 plot vicVic1
486 2016 xenLae2 GCF_001663975.1 Meraculous v. May-2013 2660 43 112843 265 1906995 50, 10, chr6S:105116072-105116181 plot xenLae2
487 2004 xenTro1 tbd tbd 140 177.5 37717 889.5 437093 94, 1, scaffold_26179:153-341 plot xenTro1
488 2005 xenTro2 tbd tbd 116 229.5 33928 806.5 320973 83, 1, scaffold_13788:6263-6429 plot xenTro2
489 2009 xenTro3 tbd tbd 116 229.5 33928 806.5 320973 83, 1, GL185958:6263-6429 plot xenTro3
490 2012 xenTro7 GCF_000004195.2 ARACHNE v. 20071016_modified 98 82.5 16149 201 69741 775, 100, KB022861:7377-9026 plot xenTro7
491 2016 xenTro9 GCF_000004195.3 Meraculous v. May-2013 172 105.5 27368 100 99243 775, 100, chrUn_NW_016684502v1:7377-9026 plot xenTro9
492 2012 xipMac1 GCF_000241075.1 PCAP v. 3/30/09; Newbler v. MapAsmResearch-02/17/2010 548 50 32896 131 334271 30, 1, JH556915:15756-15816 plot xipMac1
494 2013 zonAlb1 GCF_000385455.1 Allpaths-LG v. Feb-2013 538 79 50834 1 134738 990, 1, KB913055:7474487-7476467 plot zonAlb1

assemblies with zero duplicate gap sequences

count year dbName ncbiAsmId number of gaps assembly method
001 2012 aciBauTYTH_1 GCF_000302575.1 4 tbd
002 2006 afrOth13 tbd 220 tbd
003 2014 apaVit1 GCF_000703405.1 50921 SOAPdenovo v. 1.6
004 2018 astCal1 tbd 395 tbd
005 2006 borEut13 tbd 0 tbd
006 2014 bunEbo1 GCF_000889155.1 0 tbd
007 2010 caeJap3 tbd 0 tbd
008 2003 canFamPoodle1 GCA_000181415.1 0 tbd
009 2005 canHg12 tbd 0 tbd
010 2010 ce10 tbd 0 tbd
011 2013 ce11 GCF_000002985.6 0 tbd
012 2004 ce2 tbd 5 tbd
013 2005 ce3 tbd 0 tbd
014 2007 ce4 tbd 0 tbd
015 2007 ce5 tbd 0 tbd
016 2008 ce6 tbd 0 tbd
017 2009 ce7 tbd 0 tbd
018 2009 ce8 tbd 0 tbd
019 2010 ce9 tbd 0 tbd
020 2004 droMoj1 tbd 0 tbd
021 2014 eboVir1 tbd 2 tbd
022 2014 eboVir3 tbd 0 tbd
023 2006 euaGli13 tbd 19510 tbd
024 2006 eutHer13 tbd 304 tbd
025 2017 felCat9 GCF_000181335.3 418 WTDBG v. 1.2, Chromonomer v. 1.0.7
026 2018 galGal6 GCF_000002315.5 943 FALCON-integrate v. 1.7.5
027 1880 gasAsc0 GCA_000180675.1 0 tbd
028 2006 gliRes13 tbd 39623 tbd
029 2016 gorGor5 tbd 0 tbd
030 1993 hbv1 GCF_000861825.2 0 tbd
031 2006 homIni14 tbd 0 tbd
032 1880 homNea0 tbd 872 tbd
033 2002 hpv1 GCF_000862685.1 0 tbd
034 2006 lauRas13 tbd 31794 tbd
035 2014 marVir1 tbd 0 tbd
036 2008 melHap1 GCA_000172435.1 0 tbd
037 2008 melInc1 GCA_000180415.1 0 tbd
038 2016 oreNil3 GCF_001858045.1 424 Canu v. 1.0; Chromonomer v. 1.05
039 2006 otoGar1 tbd 0 tbd
040 2018 ponAbe3 GCF_002880775.1 553 Falcon v. (git hash: 91e700c4) Nov 2015; BioNano Access Hybrid Scaffolds
041 2008 priPac2 GCA_000180635.1 59 tbd
042 2012 repBase0 tbd 2137 tbd
043 2012 repBase1 tbd 3623 tbd
044 1880 repBase2 tbd 3237 tbd
045 2014 resEbo1 GCF_000854085.1 0 tbd
046 2016 rouAeg1 GCF_001466805.2 638 SparseAssembler v. OCTOBER-2015; DBG2OLC v. OCTOBER-2015; LINKS v. 1.5.1; L_RNA_Scaffolder v. OCTOBER-2015; SSPACE v. 3.0
047 2003 sacCer1 tbd 0 tbd
048 2008 sacCer2 tbd 0 tbd
049 2011 sacCer3 GCF_000146045.2 0 tbd
050 1880 salMan0 tbd 0 tbd
051 2006 staAur1 GCF_000013425.1 1 tbd
052 2011 strRat1 tbd 3207 tbd
053 2014 sudEbo1 GCF_000855585.1 0 tbd
054 2014 taiEbo1 GCF_000888475.1 0 tbd
055 2006 tupBel1 tbd 0 tbd
056 2014 zaiEbo1 GCF_000848505.1 0 tbd