TandemDups

methods

The measurements are taken from the tandemDups.bed[.gz] file in /hive/data/genomes/<db>/bed/tandemDups/tandemDups.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 dup 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.

tandemDups 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
019	2014	acaChl1	GCF_000695815.1	SOAPdenovo v. 1.6	69222	38	3687159		479	270396956	448, 1, KK830956:17007-17903	plot acaChl1
020	2012	aciBauTYTH_1	GCF_000302575.1	tbd	175	43	11650		1165	777735	35, 1, chr_CP003856:2714351-2714421	plot aciBauTYTH_1
021	2006	afrOth13	tbd	tbd	63170	39	3109998		1833	319093167	126, 1, 3-3:1498405-1498657	plot afrOth13
022	2013	anaPla1	GCF_000355885.1	SOAPdenovo Release v. 1.03	27792	43	2580234		401	91882502	1258, 1, KB745735:2510-5026	plot anaPla1
023	2014	ancCey1	GCA_000688135.1	Velvet v. 1.2.05; BGI GapCloser v. 1.12 (release_2011); HaploMerger v. 20111230; ERANGE v. 3.2	55040	40	3358224		389.5	157542766	4183, 1, JARK01001394v1:846761-855127	plot ancCey1
024	2003	anoGam1	tbd	tbd	75957	43	5353295		2383	356254048	1175, 1, chrX:14717656-14720006	plot anoGam1
025	2014	apaVit1	GCF_000703405.1	SOAPdenovo v. 1.6	24291	35	1216678		112	56084043	453, 1, KL385068:59340-60246	plot apaVit1
026	2004	apiMel1	tbd	tbd	83149	38	3897116		280	81345069	203, 1, GroupUn.6971:896-1302	plot apiMel1
027	2005	apiMel2	tbd	tbd	91284	38	4467103		295	110415978	234, 1, Group8:8120781-8121249	plot apiMel2
028	2005	apiMel3	tbd	tbd	100380	38	5142600		318	146199642	234, 1, Group8:9788059-9788527	plot apiMel3
029	2010	apiMel4	GCF_000002195.4	Atlas assembly system v. before 2011	101842	38	5017659		328	182902657	234, 1, Group8:11123745-11124213	plot apiMel4
030	2008	aplCal1	tbd	tbd	362965	33	14931570		1162	1691576982	254, 1, scaffold_486:233208-233716	plot aplCal1
031	1880	araTha1	GCF_000001735.3	tbd	42547	40	2336394		4141	237921318	415, 1, chr3:12226092-12226922	plot araTha1
032	2012	ascSuu1	GCA_000298755.1	SOAPdenovo v. 1.04	26863	62	2864530		136	30068625	680, 1, JH878990v1:516922-518282	plot ascSuu1
033	2014	balPav1	GCA_000709895.1	SOAPdenovo v. 1.6	17941	37	1027192		127	51713556	375, 1, KL478702:45795-46545	plot balPav1
034	2008	braFlo2	tbd	tbd	335984	40	21237833		1088	1244816809	1512, 1, Bf_V2_32:3091839-3094863	plot braFlo2
035	1880	braRap1	GCF_000309985.1	SOAPdenovo v. 1.04	74411	41	5348931		2750	314357742	1288, 2, chrA5:13328835-13331412	plot braRap1
036	2007	bruMal1	tbd	tbd	70008	37	3314327		264	46555408	321, 1, Bmal_supercontigDegenerate10576:240-882	plot bruMal1
037	2014	bruMal2	tbd	tbd	72743	38	3759073		402	111607550	453, 1, Bmal_v3_scaffold8088:119-1025	plot bruMal2
038	2014	bucRhi1	GCF_000710305.1	SOAPdenovo v. 1.6	43210	56	3393282		73	48672532	715, 1, KL533494:44624-46054	plot bucRhi1
040	2011	burXyl1	tbd	tbd	12719	36	772590		1694	51888226	134, 1, scaffold01254:876286-876554	plot burXyl1
041	2010	caeAng1	GCA_000165025.1	Velvet v. 0.7.56	100045	42	4176946		305	156635287	71, 1, scafRNAPATHr22140:12806-12948	plot caeAng1
042	2012	caeAng2	tbd	tbd	148180	41	6380576		369	202631392	131, 1, Cang_2012_03_13_00262:54689-54951	plot caeAng2
043	2008	caeJap1	tbd	tbd	54911	37	2702441		669	184995823	179, 1, chrUn:91344286-91344644	plot caeJap1
044	2009	caeJap2	tbd	tbd	61394	38	3566172		1128.5	219090212	153, 1, chrUn:143662847-143663153	plot caeJap2
045	1880	caeJap2a	tbd	tbd	59499	38	3480262		973	192672580	153, 1, Cjap_Contig3098:12088-12394	plot caeJap2a
046	2010	caeJap3	tbd	tbd	47394	36	2103165		360	75708219	176, 1, ABLE03028834:844-1196	plot caeJap3
047	2010	caeJap4	GCA_000147155.1	Celera assembler v. 6.0	66567	37	3336966		815	226847582	176, 1, Scaffold17893:329482-329834	plot caeJap4
048	2007	caePb1	tbd	tbd	67100	38	3590813		2009	281616954	168, 1, chrUn:161968878-161969214	plot caePb1
049	2008	caePb2	tbd	tbd	71710	39	3958202		3788.5	420907669	239, 1, chrUn:97561553-97562031	plot caePb2
050	2010	caePb3	GCA_000143925.2	PCAP v. 9/3/04	71721	39	3951441		3770	420080585	239, 1, Scfld02_132:346628-347106	plot caePb3
051	2005	caeRem1	tbd	tbd	78288	40	4264984		1786	318215569	193, 1, SuperCont3184:2552-2938	plot caeRem1
052	2006	caeRem2	tbd	tbd	102926	41	5484074		859	350685995	193, 1, chrUn:145434398-145434784	plot caeRem2
053	2007	caeRem3	tbd	tbd	69306	40	3736990		2408	318941600	181, 1, chrUn:147913992-147914354	plot caeRem3
054	2007	caeRem4	GCF_000149515.1	tbd	70702	39	3779779		2320	319257206	181, 1, Crem_Contig169:93478-93840	plot caeRem4
055	2010	caeSp111	GCA_000186765.1	Celera assembler v. 6.0	16576	36	783303		2230.5	70961296	161, 1, Scaffold630:3047861-3048183	plot caeSp111
056	2012	caeSp51	tbd	tbd	20559	36	877191		1869	57741956	109, 1, Csp5_scaffold_04217:6885-7103	plot caeSp51
057	2010	caeSp91	tbd	tbd	67737	36	3110776		1418	221671479	195, 1, Scaffold7109:118818-119208	plot caeSp91
058	2014	calAnn1	GCF_000699085.1	SOAPdenovo v. 1.6	115073	39	9049123		590	450885170	1104, 1, KL218440:2851016-2853224	plot calAnn1
059	2013	calMil1	GCF_000165045.1	Celera v. 6.1	365912	35	15637123		1428	1794921679	144, 1, KI635985:586597-586885	plot calMil1
060	2014	capCar1	GCF_000700745.1	SOAPdenovo v. 1.6	63810	36	3017510		389.5	221999357	1265, 2, KL360999:16916-19447	plot capCar1
061	2014	carCri1	GCF_000690535.1	SOAPdenovo v. 1.6	20461	37	1163337		68	30549622	529, 1, KK515247:46620-47678	plot carCri1
062	2002	cb1	tbd	tbd	36051	37	2442691		558	98718219	191, 1, chrUn:90311348-90311730	plot cb1
063	2005	cb2	tbd	tbd	35978	37	2444306		560	98588417	317, 1, chrIII:126724-127358	plot cb2
064	2007	cb3	tbd	tbd	35990	37	2451574		568.5	99618994	317, 1, chrIII:11646590-11647224	plot cb3
065	2011	cb4	tbd	tbd	36155	37	2519414		578	100960462	317, 1, chrIII:76433-77067	plot cb4
066	2010	ce10	tbd	tbd	33806	38	1760308		427	82769023	1500, 1, chrIV:5554976-5557976	plot ce10
067	2013	ce11	GCF_000002985.6	tbd	33816	38	1760641		427	82800067	1500, 1, chrIV:5554985-5557985	plot ce11
068	2004	ce2	tbd	tbd	33799	38	1759889		427	82752389	1500, 1, chrIV:5554978-5557978	plot ce2
069	2005	ce3	tbd	tbd	33799	38	1759889		427	82752398	1500, 1, chrIV:5554972-5557972	plot ce3
070	2007	ce4	tbd	tbd	33792	38	1759610		427	82743753	1500, 1, chrIV:5554972-5557972	plot ce4
071	2007	ce5	tbd	tbd	33794	38	1759781		427	82743927	1500, 1, chrIV:5554972-5557972	plot ce5
072	2008	ce6	tbd	tbd	33794	38	1759781		427	82743927	1500, 1, chrIV:5554972-5557972	plot ce6
073	2009	ce7	tbd	tbd	33806	38	1760308		427	82769007	1500, 1, chrIV:5554972-5557972	plot ce7
074	2009	ce8	tbd	tbd	33806	38	1760308		427	82769007	1500, 1, chrIV:5554972-5557972	plot ce8
075	2010	ce9	tbd	tbd	33806	38	1760308		427	82769007	1500, 1, chrIV:5554972-5557972	plot ce9
076	2014	chlUnd1	GCF_000695195.1	SOAPdenovo v. 1.6	28454	43	1824188		165	94696650	497, 1, KK750077:105999-106993	plot chlUnd1
077	2002	ci1	GCA_000183065.1	tbd	48663	39	2653274		626	122189601	486, 1, Scaffold_604:30085-31057	plot ci1
078	2005	ci2	tbd	tbd	119965	43	8287326		1961	566064667	358, 1, scaffold_83:159982-160698	plot ci2
079	2011	ci3	GCF_000224145.1	tbd	48178	39	2574684		692	149951145	486, 1, chrUn_NW_004190340v1:65099-66071	plot ci3
080	2003	cioSav1	tbd	tbd	123843	39	6363601		2503	618224769	189, 1, ps_297:30448-30826	plot cioSav1
081	2005	cioSav2	tbd	tbd	157468	38	7731855		2875	819500559	280, 1, reftig_238:125039-125599	plot cioSav2
082	2013	colLiv1	GCF_000337935.1	SOAPdenovo v. 2.0	139510	33	6394287		112	419571584	3080, 2, KB375367:1029739-1035900	plot colLiv1
083	2014	colStr1	GCF_000690715.1	SOAPdenovo v. 1.6	55406	40	3066780		131	154687137	309, 1, KK533057:6873-7491	plot colStr1
084	2014	corBra1	GCF_000691975.1	SOAPdenovo v. 1.6	91630	37	6371852		297	248570100	1583, 1, KK718913:5901493-5904659	plot corBra1
085	2014	corCor1	GCF_000738735.1	AllPaths v. Allpaths-LG version 41687	58556	36	3043376		370	184023111	1935, 1, KL997525:15617964-15621834	plot corCor1
086	2013	cotJap1	GCA_000511605.1	Soapdenovo v. 1.0.5b; bwa v. 0.5.9; SSPACE v. 1.2	7329	33	280548		75	2914174	214, 1, DF262918:84572-85000	plot cotJap1
087	2014	cucCan1	GCF_000709325.1	SOAPdenovo v. 1.6	126008	42	16101261		2142	633238955	2278, 1, KL448309:4464943-4469499	plot cucCan1
088	2014	cynSem1	GCF_000523025.1	SOAPdenovo v. April-2011	83655	37	6369004		261	184971677	1536, 1, chr1:16715796-16718868	plot cynSem1
089	2014	cypVar1	GCA_000732505.1	AllPaths v. May 2014	136313	39	9823682		1299	502219020	2138, 1, KL652705:564642-568918	plot cypVar1
090	2014	dicLab1	GCA_000689215.1	tbd	204757	36	11489728		924	691437386	841, 1, HG916851:32290203-32291885	plot dicLab1
091	2013	dirImm1	tbd	tbd	3309	36	316992		58	1820327	1613, 1, nDi_2_2_scaf00284:19002-22228	plot dirImm1
092	2003	dm1	tbd	tbd	12199	50	1260685		3445	60460276	3882, 2, chr2L:1894810-1902575	plot dm1
093	2004	dm2	tbd	tbd	13213	51	1372092		3723	67342596	3882, 2, chr2L:1893145-1900910	plot dm2
094	2006	dm3	tbd	tbd	113222	40	6787673		2412	622002007	3882, 2, chr2L:1893145-1900910	plot dm3
095	2014	dm6	GCF_000001215.4	tbd	48031	48	4403254		3448	254474999	3882, 2, chr2L:1893145-1900910	plot dm6
096	2003	dp2	tbd	tbd	16790	44	1110948		926	42217528	227, 1, Contig7446_Contig2444:1979445-1979899	plot dp2
097	2004	dp3	tbd	tbd	20334	44	1389766		1239	62703720	312, 1, chrU:9357988-9358612	plot dp3
098	2006	dp4	tbd	tbd	53060	46	3495255		2437	228127096	312, 1, Unknown_singleton_2460:32411-33035	plot dp4
099	2012	droAlb1	GCA_000298335.1	SOAPdenovo v. 1.04	126521	30	3970849		70	35343627	76, 1, JH853217:889-1041	plot droAlb1
100	2004	droAna1	tbd	tbd	67882	40	3659056		697	196198368	572, 1, 2446670:645-1789	plot droAna1
101	2005	droAna2	tbd	tbd	248263	42	14624595		918	748771139	572, 1, scaffold_13499:1095908-1097052	plot droAna2
102	2006	droAna3	GCF_000005115.1	tbd	246334	42	14515690		927	745835855	572, 1, scaffold_13499:1092668-1093812	plot droAna3
103	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	46906	42	2807408		2591	175612579	2241, 3, AFFD02006372:54233-58717	plot droBia2
104	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	54693	39	2946335		1371	204354268	179, 1, KB463958:131929-132287	plot droBip2
105	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	34862	41	2092385		2187	135919965	270, 1, KB458613:1953986-1954526	plot droEle2
106	2005	droEre1	tbd	tbd	96336	44	5585722		674	191777516	359, 1, scaffold_1301:371-1089	plot droEre1
107	2006	droEre2	GCF_000005135.1	tbd	95081	44	5535640		676	190524603	359, 1, scaffold_1301:371-1089	plot droEre2
108	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	59111	40	3495099		1518	181127987	141, 1, KB464979:6084-6366	plot droEug2
109	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	21964	44	1418464		2380.5	83742114	190, 1, AFFG02001364:4041-4421	plot droFic2
110	2005	droGri1	tbd	tbd	458551	40	21432909		509	538034457	491, 1, scaffold_2211:899-1881	plot droGri1
111	2006	droGri2	GCF_000005155.2	tbd	302510	40	14467041		522	418546843	188, 1, scaffold_6592:1167-1543	plot droGri2
112	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	31358	41	1855833		1533.5	112074726	117, 1, KB459586:778466-778700	plot droKik2
113	2013	droMir2	GCA_000269505.2	Newbler v. 2.6	18368	45	1204033		1747	75101816	140, 1, chr2:3040735-3041015	plot droMir2
114	2004	droMoj1	tbd	tbd	69928	38	3220037		310	78711524	225, 1, contig_34282:247-697	plot droMoj1
115	2005	droMoj2	tbd	tbd	102140	41	5658627		1086	363630258	202, 1, scaffold_6540:14391223-14391627	plot droMoj2
116	2006	droMoj3	GCF_000005175.2	tbd	101230	41	5606832		1114	361818537	202, 1, scaffold_6540:14384339-14384743	plot droMoj3
117	2005	droPer1	GCF_000005195.2	tbd	75046	45	5536401		2595	325634621	580, 2, super_62:246420-247581	plot droPer1
118	2013	droPse3	GCF_000001765.3	PBJelly v. 12.8.2; Atlas genome assembly	53481	45	3494617		2480	231367590	312, 1, chrUn_CH674897_1:32411-33035	plot droPse3
119	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	68118	41	4002283		1672	235074913	205, 1, AFPP02028413:1419-1829	plot droRho2
120	2005	droSec1	GCA_000005215.1	tbd	127886	38	6652375		465	177925676	360, 1, super_6483:1086-1806	plot droSec1
121	2005	droSim1	tbd	tbd	47915	42	2874159		1400	171101666	217, 1, chr3R_random:168062-168496	plot droSim1
122	2014	droSim2	GCF_000754195.2	Velvet v. 1.1.04	10385	40	551061		466	26120972	217, 1, chrUn_NW_015496898v1:4674-5108	plot droSim2
123	2013	droSuz1	GCA_000472105.1	SOAPdenovo v. 2	117859	46	12342639		2277	517597655	4939, 1, KI419149:2637663-2647541	plot droSuz1
124	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	48870	41	2816693		2013	202395837	306, 1, AFFI02002878:4290-4902	plot droTak2
125	2004	droVir1	tbd	tbd	147648	35	6630839		429	239695710	244, 1, scaffold_0:5707381-5707869	plot droVir1
126	2005	droVir2	tbd	tbd	432783	30	17539885		481	757905036	244, 1, scaffold_13049:18877549-18878037	plot droVir2
127	2006	droVir3	GCF_000005245.1	tbd	407188	30	16757243		495	747769004	244, 1, scaffold_13049:18848863-18849351	plot droVir3
128	2006	droWil1	GCF_000005925.1	tbd	118355	42	7234894		1695	472632964	954, 1, scaffold_181130:9135849-9137757	plot droWil1
129	2006	droWil2	GCF_000005925.1	tbd	118240	42	7228999		1695	472142234	954, 1, CH964272:9135849-9137757	plot droWil2
130	2004	droYak1	tbd	tbd	81563	43	6228480		3752	459910434	851, 1, chr3L:24830341-24832043	plot droYak1
131	2005	droYak2	tbd	tbd	93441	45	6941572		3518	501527798	1122, 2, chrU:731511-733756	plot droYak2
132	2006	droYak3	GCF_000005975.2	tbd	85136	46	6497582		2641	404384429	1122, 2, chrUn_CH892674_1:731511-733756	plot droYak3
135	2014	esoLuc1	GCA_000721915.1	AllPaths v. 43500	309026	36	12717997		109	633934424	1803, 1, KL593524:286555-290161	plot esoLuc1
136	2014	eurHel1	GCF_000690775.1	SOAPdenovo v. 1.6	48033	41	2646849		3690	271468700	462, 1, KK561721:27808-28732	plot eurHel1
137	2002	fr1	tbd	tbd	65564	35	3413218		165	124234021	304, 1, chrUn:169005183-169005791	plot fr1
138	2004	fr2	tbd	tbd	104956	35	5519798		156	261084207	151, 1, chrUn:356162839-356163141	plot fr2
139	2011	fr3	GCF_000180615.1	tbd	105765	35	5702900		157	257018230	151, 1, HE592488:202-504	plot fr3
140	2010	gadMor1	GCA_000231765.1	tbd	523023	30	17042881		24	573821154	131, 1, HE571852:62524-62786	plot gadMor1
141	2004	galGal2	tbd	tbd	157813	51	15224008		3723	846924205	208, 1, chr2:94743278-94743694	plot galGal2
142	2006	galGal3	tbd	tbd	243371	62	25066425		3004	1138149811	208, 1, chr2:97262115-97262531	plot galGal3
143	2011	galGal4	GCF_000002315.3	Celera Assembler v. 5.4	78961	39	4732239		2968	493569103	17591, 16, chrZ:21320544-21355741	plot galGal4
144	2006	gasAcu1	tbd	tbd	131262	39	7836949		3635	770629287	296, 1, chrUn:59780312-59780904	plot gasAcu1
145	1880	gasAsc0	GCA_000180675.1	tbd	116031	39	6613325		1417	518945407	316, 1, contig_16726:674-1306	plot gasAsc0
146	2014	gavSte1	GCF_000690875.1	SOAPdenovo v. 1.6	24295	36	1352476		75	47417993	302, 1, KK611813:2739-3343	plot gavSte1
147	2012	geoFor1	GCF_000277835.1	SOAPdenovo v. 2.01	113187	37	6785044		204	268468600	1013, 1, JH739970:2776008-2778034	plot geoFor1
148	2006	gliRes13	tbd	tbd	31976	36	1385928		1661	143989628	95, 1, 4-7:15697982-15698172	plot gliRes13
149	2016	gorGor5	tbd	tbd	3555119	33	133654191		4102	21270991545	338, 1, CYUI01005848v1:13590-14266	plot gorGor5
150	2009	haeCon1	tbd	tbd	109810	42	5802860		1251.5	319005845	196, 1, Hcon_Contig0025586:3955-4347	plot haeCon1
151	2013	haeCon2	tbd	tbd	53818	43	3892613		570	187299643	2147, 1, scaffold_1557:10532-14826	plot haeCon2
152	2014	halAlb1	GCF_000691405.1	SOAPdenovo v. 1.6	13685	36	754065		301	41720730	548, 2, KK653364:30569-31666	plot halAlb1
153	2014	halLeu1	GCF_000737465.1	SOAPdenovo2 v. May 2014	16099	40	1241068		4586	98353830	79, 1, KL869431:1084034-1084192	plot halLeu1
154	2011	hapBur1	GCF_000239415.1	ALLPATHS-LG v. R35951	34584	37	2342045		3524.5	202958431	10390, 20, JH425331:1373378-1394177	plot hapBur1
155	2011	hetBac1	GCA_000223415.1	Celera assembler v. 6.0	3302	51	353946		673	12041725	317, 1, GL996135v1:102345-102979	plot hetBac1
156	1880	homNea0	tbd	tbd	148	30	4725		14.5	2669	37, 1, 151586_3339_2553:20-94	plot homNea0
158	2011	lepOcu1	GCF_000242695.1	AllPaths v. R38293	77276	37	4579890		1084	350156295	488, 2, chrLG5:14840992-14841969	plot lepOcu1
159	2013	letCam1	GCA_000466285.1	Newbler v. 2.7	768187	35	32420899		153	1525909318	207, 1, KE997215:997-1411	plot letCam1
160	1880	linHum0	GCF_000217595.1	CABOG v. 5.3	42080	41	2313367		5018	259661061	101, 1, NW_012160424:64875-65077	plot linHum0
161	2012	loaLoa1	GCA_000183805.3	Newbler v. 2.1-PreRelease-4/28/2009	15889	37	1294459		188	16478676	109, 1, JH717180v1:404-622	plot loaLoa1
163	2012	mayZeb1	GCF_000238955.1	AllPaths v. R37043	48899	38	3205287		4159	307830483	9605, 105, JH720664:938440-957754	plot mayZeb1
164	2009	melGal1	tbd	tbd	25253	45	1794885		2825	133788059	169, 1, chr3:54352580-54352918	plot melGal1
165	2008	melHap1	GCA_000172435.1	tbd	12515	41	832837		375	21806223	157, 1, MhA1_Contig2844:850-1164	plot melHap1
166	2008	melInc1	GCA_000180415.1	tbd	19330	40	1244828		558	47252172	183, 1, Minc_Contig6373:3669-4035	plot melInc1
167	2008	melInc2	tbd	tbd	22743	41	1594354		1067	83086394	183, 1, MiV1ctg2756:3669-4035	plot melInc2
168	2011	melUnd1	GCF_000238935.1	Celera v. 6.1	99875	41	5463070		6271	754338919	120, 1, JH556605:5210251-5210491	plot melUnd1
169	2014	merNub1	GCF_000691845.1	SOAPdenovo v. 1.6	37279	43	2280064		174	103616988	543, 1, KK705997:21022-22108	plot merNub1
170	2014	mesUni1	GCF_000695765.1	SOAPdenovo v. 1.6	52863	36	2585696		257	120590969	271, 1, JJRI01098248:16372-16914	plot mesUni1
171	2013	musDom2	GCF_000371365.1	AllPathsLG v. September 2012	575203	36	27589830		1941	2513509860	2028, 1, KB856326:64184-68240	plot musDom2
172	2013	necAme1	GCF_000507365.1	Newbler v. MapAsmResearch-04/19/2010-patch-08/17/2010	30870	43	1735538		1580	123448969	93, 1, KI659398v1:132-318	plot necAme1
173	2007	nemVec1	tbd	tbd	540729	40	30645450		589	1501673463	353, 1, scaffold_201:423580-424286	plot nemVec1
174	2011	neoBri1	GCF_000239395.1	ALLPATHS-LG v. R36800	62939	46	6697998		1655	274117853	8242, 20, JH422273:8382583-8399086	plot neoBri1
175	2014	notCor1	GCF_000735185.1	Celera Assembler v. 7.0	164483	34	7109993		199	393266432	407, 1, KL665414:596304-597118	plot notCor1
176	2013	oncVol1	GCA_000499405.1	tbd	5247	39	423838		2124	28089581	739, 1, HG738137v1:12037947-12039425	plot oncVol1
177	2011	oreNil1	tbd	tbd	80799	39	4892346		6067	586359236	9755, 32, GL831139:3510855-3530396	plot oreNil1
178	2006	oryLat1	tbd	tbd	191645	40	12487530		1210	620191379	379, 1, chr9:5041681-5042439	plot oryLat1
179	2005	oryLat2	tbd	tbd	189087	40	12356700		1234	592910738	379, 1, chr9:5041681-5042439	plot oryLat2
180	2013	panRed1	GCA_000341325.1	Velvet v. 1.2.07	23300	42	1084666		1396	66559726	101, 1, KB454925:8492-8694	plot panRed1
181	2007	petMar1	tbd	tbd	855653	36	38339527		201	932728649	362, 1, Contig99174:237-961	plot petMar1
182	2010	petMar2	GCA_000148955.1	Arachne v. 3.2	836219	37	38092404		692	2324558773	363, 1, GL498477:1987-2713	plot petMar2
183	2014	picPub1	GCF_000699005.1	SOAPdenovo v. 1.6	397798	36	17968999		7796	3299119050	4915, 3, KL215520:252741-262573	plot picPub1
184	2013	poeFor1	GCF_000485575.1	AllPaths-LG v. July 2013	161806	52	28441594		4650	990605574	1886, 1, KI520679:7484-11256	plot poeFor1
185	2014	poeRet1	tbd	tbd	71291	38	4816409		1511	343849361	8790, 4, chrLG5:27506035-27523618	plot poeRet1
186	2014	priExs1	tbd	tbd	33878	44	2639333		1128	98936342	1626, 1, scaffold830:51430-54682	plot priExs1
187	2007	priPac1	tbd	tbd	29257	43	1929264		448	80615899	500, 1, chrUn:71534792-71535792	plot priPac1
188	2008	priPac2	GCA_000180635.1	tbd	19318	39	1050200		259	25863820	500, 1, ABKE01002096:3239-4239	plot priPac2
189	2014	priPac3	tbd	tbd	36759	40	2176431		321	82136541	500, 1, Ppa_Contig5:941324-942324	plot priPac3
190	2013	pseHum1	GCF_000331425.1	SOAPdenovo v. 1.5	140033	36	7836448		130	200423267	7517, 10, KB221191:4083820-4098863	plot pseHum1
191	2014	pteGut1	GCF_000699245.1	SOAPdenovo v. 1.6	41594	36	2007893		100	106772284	534, 1, JMFR01060883:1891-2959	plot pteGut1
192	2011	punNye1	GCF_000239375.1	ALLPATHS-LG v. R37016	36249	38	2385815		3630	214952201	5131, 20, JH419262:1608400-1618681	plot punNye1
193	2012	repBase0	tbd	tbd	54	39	2426		81.5	7619	70, 1, MER51A:232-372	plot repBase0
194	2012	repBase1	tbd	tbd	73	39	3249		77	9691	70, 1, MER51A:232-372	plot repBase1
195	1880	repBase2	tbd	tbd	51	40	2203		79	6907	70, 1, MER51A:232-372	plot repBase2
197	1880	ricCom1	GCF_000151685.1	tbd	430308	35	18638247		2948	2156357980	460, 1, EQ974418:17730-18650	plot ricCom1
198	2003	sacCer1	tbd	tbd	666	45	76615		1914.5	2711249	50, 1, chr7:519107-519207	plot sacCer1
199	2008	sacCer2	tbd	tbd	669	45	76812		1868	2711600	71, 1, chrX:120898-121040	plot sacCer2
200	2011	sacCer3	GCF_000146045.2	tbd	669	45	78716		1868	2711582	1988, 10, chrVIII:212266-216251	plot sacCer3
201	2013	sebNig1	GCA_000475235.1	tbd	344468	43	18020844		94	249080272	492, 1, AUPR01114153:357-1341	plot sebNig1
202	2013	sebRub1	GCA_000475215.1	SOAPdenovo v. 1.05	299208	38	14417679		139	352997550	408, 1, KI445670:61530-62346	plot sebRub1
203	2014	stePar1	GCF_000690725.1	ALLPATHS-LG v. August 2013	96483	40	8151514		3673	549500672	2624, 1, KK581067:134955-140203	plot stePar1
204	2005	strPur1	tbd	tbd	658932	40	35574440		847.5	1824767726	956, 1, Scaffold18311:2619-4531	plot strPur1
205	2006	strPur2	tbd	tbd	611722	39	30968979		1453	2323533345	956, 1, Scaffold47464:201872-203784	plot strPur2
206	2009	strPur3	tbd	tbd	689739	40	35781206		1763	2733632009	956, 1, Scaffold85:237230-239142	plot strPur3
207	2011	strPur4	GCF_000002235.3	Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement	888256	42	54558021		2360	3918297070	956, 1, Scaffold382:244159-246071	plot strPur4
208	2011	strRat1	tbd	tbd	9910	40	540468		1077	26058414	113, 1, RATTI_contig_57682:4110-4336	plot strRat1
209	2014	strRat2	GCA_001040885.1	tbd	8546	41	482721		2233	37502032	67, 1, chrUn_LN609483v1:243-377	plot strRat2
211	1880	taeGut0	tbd	tbd	597003	49	43955858		3833	2936709220	209, 1, Contig47:5328655-5329073	plot taeGut0
212	2013	taeGut2	GCF_000151805.1	PCAP v. 2008	602028	49	44591081		3541	2830875406	209, 1, chrZ:28813941-28814359	plot taeGut2
214	2013	takFla1	GCA_000400755.1	HAPs v. 0.2.2	97724	36	6776388		184	251435705	503, 1, KE121297:329-1335	plot takFla1
215	2004	tetNig1	tbd	tbd	132260	38	9178877		3055	661840431	413, 1, chrUn_random:43732955-43733781	plot tetNig1
216	2007	tetNig2	tbd	tbd	130250	38	9072570		3013	657839855	413, 1, chrUn_random:35610230-35611056	plot tetNig2
217	2014	tinGut1	GCF_000705375.1	SOAPdenovo v. 1.6	43221	38	2742653		279	110109614	416, 1, KL400833:106660-107492	plot tinGut1
218	2014	tinGut2	GCF_000705375.1	SOAPdenovo v. 1.6	43210	38	2741340		279	110101482	416, 1, KL895505:106660-107492	plot tinGut2
219	2005	triCas1	tbd	tbd	78796	41	4117576		794	170185880	307, 1, Reptig797:115-729	plot triCas1
220	2005	triCas2	tbd	tbd	77889	41	4122780		885	196279053	192, 1, singleUn_1374:29986-30370	plot triCas2
221	2011	triSpi1	GCF_000181795.1	PCAP v. January 12, 2007	11343	54	1176023		4572	74727382	98, 1, GL622792v1:5540185-5540381	plot triSpi1
222	2014	triSui1	GCA_000701005.1	SOAPdenovo v. 2	17372	45	1593967		2042.5	75416120	501, 1, KL363185v1:221782-222784	plot triSui1
223	2014	tytAlb1	GCF_000687205.1	SOAPdenovo v. 1.6	15140	33	776246		81	23744286	199, 1, JJRD01024771:5513-5911	plot tytAlb1
224	2012	xipMac1	GCF_000241075.1	PCAP v. 3/30/09; Newbler v. MapAsmResearch-02/17/2010	39708	35	1764516		506	136874274	119, 1, JH557910:3615-3853	plot xipMac1
226	2013	zonAlb1	GCF_000385455.1	Allpaths-LG v. Feb-2013	220251	35	9228906		369	407868591	2060, 1, KB913045:8123897-8128017	plot zonAlb1

assemblies with zero duplicate gap sequences

count	year	dbName	ncbiAsmId	number of gaps	assembly method