GeoFor1 Genome size statistics: Difference between revisions
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQF00 Zebra finch]</TD><TH ALIGN=CENTER>6X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQF00 Zebra finch]</TD><TH ALIGN=CENTER>6X</TH> | ||
<TH ALIGN=CENTER>73657157</TH> | <TH ALIGN=CENTER>73657157</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>92.532%</TD> | ||
<TD ALIGN=RIGHT>1000</TD> | <TD ALIGN=RIGHT>1000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/111 | <TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/10765 03]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]</TH> | ||
<TH ALIGN=RIGHT>25,212</TH> | |||
<TD ALIGN=RIGHT>1,117,373,619</TD><TD ALIGN=RIGHT>1,086,614,815</TD> | |||
<TD ALIGN=RIGHT>30,758,804</TD><TD ALIGN=RIGHT>% 19.62</TD> | |||
<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGAI01 Budgerigar]</TD><TH ALIGN=CENTER>7X</TH> | |||
<TH ALIGN=CENTER>10614383</TH> | |||
<TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>80.650%</TD> | |||
<TD ALIGN=RIGHT>1000</TD> | |||
<TD ALIGN=CENTER>loose</TD></TR> | |||
<TR><TH ALIGN=RIGHT>[http://www.ncbi.nlm.nih.gov/genome/111 04]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]</TH> | |||
<TH ALIGN=RIGHT>15,932</TH> | <TH ALIGN=RIGHT>15,932</TH> | ||
<TD ALIGN=RIGHT>1,046,932,099</TD><TD ALIGN=RIGHT>1,032,854,810</TD> | <TD ALIGN=RIGHT>1,046,932,099</TD><TD ALIGN=RIGHT>1,032,854,810</TD> | ||
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Chicken]</TD><TH ALIGN=CENTER>12X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AADN00 Chicken]</TD><TH ALIGN=CENTER>12X</TH> | ||
<TH ALIGN=CENTER>90216835</TH> | <TH ALIGN=CENTER>90216835</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>70.718%</TD> | ||
<TD ALIGN=RIGHT>1000</TD> | <TD ALIGN=RIGHT>1000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
<TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ | <TR><TH ALIGN=RIGHT>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Meleagris_gallopavo/Turkey_2.01/ 05]</TH><TH ALIGN=RIGHT>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]</TH> | ||
<TH ALIGN=RIGHT>5,891</TH> | <TH ALIGN=RIGHT>5,891</TH> | ||
<TD ALIGN=RIGHT>1,061,817,101</TD><TD ALIGN=RIGHT>935,922,386</TD> | <TD ALIGN=RIGHT>1,061,817,101</TD><TD ALIGN=RIGHT>935,922,386</TD> | ||
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ADDD00 Turkey]</TD><TH ALIGN=CENTER>5X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ADDD00 Turkey]</TD><TH ALIGN=CENTER>5X</TH> | ||
<TH ALIGN=CENTER>74864452</TH> | <TH ALIGN=CENTER>74864452</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>SyntenicNet</TH><TD ALIGN=RIGHT>67.079%</TD> | ||
<TD ALIGN=RIGHT>1000</TD> | <TD ALIGN=RIGHT>1000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human]</TD><TH ALIGN=CENTER>20X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human]</TD><TH ALIGN=CENTER>20X</TH> | ||
<TH ALIGN=CENTER>146364022</TH> | <TH ALIGN=CENTER>146364022</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>8.504%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
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<TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mouse]</TD><TH ALIGN=CENTER>20X</TH> | <TD ALIGN=CENTER>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mouse]</TD><TH ALIGN=CENTER>20X</TH> | ||
<TH ALIGN=CENTER>130694993</TH> | <TH ALIGN=CENTER>130694993</TH> | ||
<TH ALIGN=CENTER> | <TH ALIGN=CENTER>RecipBest</TH><TD ALIGN=RIGHT>7.709%</TD> | ||
<TD ALIGN=RIGHT>5000</TD> | <TD ALIGN=RIGHT>5000</TD> | ||
<TD ALIGN=CENTER>loose</TD></TR> | <TD ALIGN=CENTER>loose</TD></TR> | ||
</TABLE> | </TABLE> | ||
Revision as of 23:26, 2 August 2012
see also
- Medium ground finch 7-way GeoFor1 conservation alignment
- Medium ground finch 7-way GeoFor1 conservation lastz parameters
- all other UCSC Multiple Alignments
statistics collected from UCSC 2bit files
- The external link in the first column goes to the FTP location where the genome sequence was obtained
- The external links from the UCSC database name go to the UCSC genome-test browser for that genome
- N bases == unknown bases in the assembly marked by "N"
- non-N bases == called bases in the assembly
- total size == all bases in assembly, N and non-N
- The % masked is masking from Repeat Masker or Window Masker plus TRF/Simple Repeats, whichever is greater, usually WindowMasker for these genomes
- The common name external links go to information pages for this genome
- The coverage numbers are taken directly from information README files from the sequencing center
- The N50 size is calculated directly from the UCSC chrom.sizes file which is the size of the chromosomes as seen in the UCSC genome browser
do not edit, automatically generated table
| order count/ ftp src |
ucsc db name/ genome-test |
chrom count |
total size |
non-N bases |
N base count |
% masked | common name/ src info |
coverage | N50 chrom.sizes |
alignment type | % of geoFor1 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | geoFor1 | 27,239 | 1,065,292,181 | 1,041,286,029 | 24,006,152 | % 19.99 | Medium ground finch | 115X | 5255844 | N/A | N/A | N/A | N/A |
| 02 | taeGut1 | 70 | 1,233,186,341 | 1,222,864,691 | 10,321,650 | % 20.42 | Zebra finch | 6X | 73657157 | SyntenicNet | 92.532% | 1000 | loose |
| 03 | melUnd1 | 25,212 | 1,117,373,619 | 1,086,614,815 | 30,758,804 | % 19.62 | Budgerigar | 7X | 10614383 | SyntenicNet | 80.650% | 1000 | loose |
| 04 | galGal4 | 15,932 | 1,046,932,099 | 1,032,854,810 | 14,077,289 | % 20.41 | Chicken | 12X | 90216835 | SyntenicNet | 70.718% | 1000 | loose |
| 05 | melGal1 | 5,891 | 1,061,817,101 | 935,922,386 | 125,894,715 | % 6.60 | Turkey | 5X | 74864452 | SyntenicNet | 67.079% | 1000 | loose |
| 06 | hg19 | 93 | 3,137,161,264 | 2,897,310,462 | 239,850,802 | % 50.63 | Human | 20X | 146364022 | RecipBest | 8.504% | 5000 | loose |
| 07 | mm10 | 66 | 2,730,871,774 | 2,652,783,500 | 78,088,274 | % 45.18 | Mouse | 20X | 130694993 | RecipBest | 7.709% | 5000 | loose |
