Hg38 27-way Genome size statistics: Difference between revisions
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! % masked | ! % masked | ||
! common name<br>src info | ! common name<br>src info | ||
! coverage | ! coverage<br>X | ||
! N50<br>chrom.sizes | ! N50<br>chrom.sizes | ||
! alignment type | ! alignment type | ||
| Line 47: | Line 47: | ||
| % 52.10 | | % 52.10 | ||
| [http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human] | | [http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Human] | ||
! | ! 20 | ||
! 145138636 | ! 145138636 | ||
! N/A | ! N/A | ||
| Line 62: | Line 62: | ||
| % 52.72 | | % 52.72 | ||
| [https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AACZ04 Chimp] | | [https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AACZ04 Chimp] | ||
! | ! 6 | ||
! 135926727 | ! 135926727 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 77: | Line 77: | ||
| % 50.59 | | % 50.59 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Pan_paniscus/all_assembly_versions/GCF_000258655.2_panpan1.1/ Bonobo] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Pan_paniscus/all_assembly_versions/GCF_000258655.2_panpan1.1/ Bonobo] | ||
! | ! 26 | ||
! 144709823 | ! 144709823 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 92: | Line 92: | ||
| % 50.02 | | % 50.02 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Gorilla_gorilla/all_assembly_versions/GCA_900006655.1_GSMRT3/ Gorilla] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Gorilla_gorilla/all_assembly_versions/GCA_900006655.1_GSMRT3/ Gorilla] | ||
! | ! 71 | ||
! 10016017 | ! 10016017 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 107: | Line 107: | ||
| % 50.89 | | % 50.89 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABGA00 Orangutan] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABGA00 Orangutan] | ||
! | ! 6 | ||
! 135191526 | ! 135191526 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 122: | Line 122: | ||
| % 51.14 | | % 51.14 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Nomascus_leucogenys/Nleu_3.0/ Gibbon] | | [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Nomascus_leucogenys/Nleu_3.0/ Gibbon] | ||
! 5. | ! 5.6 | ||
! 117381234 | ! 117381234 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 137: | Line 137: | ||
| % 54.33 | | % 54.33 | ||
| [https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JSUE03 Rhesus] | | [https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JSUE03 Rhesus] | ||
! 47. | ! 47.4 | ||
! 144306982 | ! 144306982 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 152: | Line 152: | ||
| % 50.11 | | % 50.11 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Macaca_fascicularis/Macaca_fascicularis_5.0/ Crab-eating macaque] | | [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Macaca_fascicularis/Macaca_fascicularis_5.0/ Crab-eating macaque] | ||
! | ! 68 | ||
! 152835861 | ! 152835861 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 167: | Line 167: | ||
| % 50.07 | | % 50.07 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_nemestrina/all_assembly_versions/GCF_000956065.1_Mnem_1.0/ Pig-tailed macaque] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_nemestrina/all_assembly_versions/GCF_000956065.1_Mnem_1.0/ Pig-tailed macaque] | ||
! 113. | ! 113.1 | ||
! 15219753 | ! 15219753 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 182: | Line 182: | ||
| % 49.92 | | % 49.92 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Cercocebus_atys/all_assembly_versions/GCF_000955945.1_Caty_1.0/ Sooty mangabey] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Cercocebus_atys/all_assembly_versions/GCF_000955945.1_Caty_1.0/ Sooty mangabey] | ||
! | ! 192 | ||
! 12849131 | ! 12849131 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 197: | Line 197: | ||
| % 52.40 | | % 52.40 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Papio_anubis/all_assembly_versions/GCF_000264685.2_Panu_2.0/ Baboon] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Papio_anubis/all_assembly_versions/GCF_000264685.2_Panu_2.0/ Baboon] | ||
! | ! 85 | ||
! 139646187 | ! 139646187 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 212: | Line 212: | ||
| % 48.77 | | % 48.77 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AQIB01 Green monkey] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AQIB01 Green monkey] | ||
! | ! 95 | ||
! 101219884 | ! 101219884 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 227: | Line 227: | ||
| % 49.47 | | % 49.47 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mandrillus_leucophaeus/all_assembly_versions/GCF_000951045.1_Mleu.le_1.0/ Drill] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mandrillus_leucophaeus/all_assembly_versions/GCF_000951045.1_Mleu.le_1.0/ Drill] | ||
! 117. | ! 117.2 | ||
! 3186748 | ! 3186748 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 242: | Line 242: | ||
| % 46.33 | | % 46.33 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JMHX01 Proboscis monkey] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JMHX01 Proboscis monkey] | ||
! | ! 290 | ||
! 137426304 | ! 137426304 | ||
! RecipBest | ! RecipBest | ||
| Line 257: | Line 257: | ||
| % 49.72 | | % 49.72 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Colobus_angolensis/all_assembly_versions/GCF_000951035.1_Cang.pa_1.0/ Angolan colobus] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Colobus_angolensis/all_assembly_versions/GCF_000951035.1_Cang.pa_1.0/ Angolan colobus] | ||
! 86. | ! 86.8 | ||
! 7840981 | ! 7840981 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 272: | Line 272: | ||
| % 51.07 | | % 51.07 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JABR01 Golden snub-nosed monkey] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JABR01 Golden snub-nosed monkey] | ||
! 53. | ! 53.7 | ||
! 1549224 | ! 1549224 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 287: | Line 287: | ||
| % 50.27 | | % 50.27 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Rhinopithecus_bieti/all_assembly_versions/GCF_001698545.1_ASM169854v1/ Black snub-nosed monkey] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Rhinopithecus_bieti/all_assembly_versions/GCF_001698545.1_ASM169854v1/ Black snub-nosed monkey] | ||
! 76. | ! 76.6 | ||
! 2225337 | ! 2225337 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 302: | Line 302: | ||
| % 47.71 | | % 47.71 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ACFV00 Marmoset] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ACFV00 Marmoset] | ||
! | ! 6 | ||
! 132174527 | ! 132174527 | ||
! RecipBest | ! RecipBest | ||
| Line 317: | Line 317: | ||
| % 46.69 | | % 46.69 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGCE01 Squirrel monkey] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AGCE01 Squirrel monkey] | ||
! | ! 80 | ||
! 18744880 | ! 18744880 | ||
! RecipBest | ! RecipBest | ||
| Line 332: | Line 332: | ||
| % 47.29 | | % 47.29 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Cebus_capucinus/all_assembly_versions/GCF_001604975.1_Cebus_imitator-1.0/ White-faced sapajou] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Cebus_capucinus/all_assembly_versions/GCF_001604975.1_Cebus_imitator-1.0/ White-faced sapajou] | ||
! | ! 81 | ||
! 5274112 | ! 5274112 | ||
! RecipBest | ! RecipBest | ||
| Line 347: | Line 347: | ||
| % 47.38 | | % 47.38 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Aotus_nancymaae/all_assembly_versions/GCF_000952055.2_Anan_2.0/ Ma's night monkey] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Aotus_nancymaae/all_assembly_versions/GCF_000952055.2_Anan_2.0/ Ma's night monkey] | ||
! 132. | ! 132.4 | ||
! 8268663 | ! 8268663 | ||
! RecipBest | ! RecipBest | ||
| Line 362: | Line 362: | ||
| % 47.85 | | % 47.85 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRT02 Tarsier] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABRT02 Tarsier] | ||
! | ! 48 | ||
! 401181 | ! 401181 | ||
! SyntenicNet | ! SyntenicNet | ||
| Line 377: | Line 377: | ||
| % 41.27 | | % 41.27 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Microcebus_murinus/all_assembly_versions/GCF_000165445.2_Mmur_3.0/ Mouse lemur] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Microcebus_murinus/all_assembly_versions/GCF_000165445.2_Mmur_3.0/ Mouse lemur] | ||
! 221. | ! 221.6 | ||
! 108171978 | ! 108171978 | ||
! RecipBest | ! RecipBest | ||
| Line 392: | Line 392: | ||
| % 39.39 | | % 39.39 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Propithecus_coquereli/all_assembly_versions/GCF_000956105.1_Pcoq_1.0/ Coquerel's sifaka] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Propithecus_coquereli/all_assembly_versions/GCF_000956105.1_Pcoq_1.0/ Coquerel's sifaka] | ||
! 104. | ! 104.7 | ||
! 5604909 | ! 5604909 | ||
! RecipBest | ! RecipBest | ||
| Line 407: | Line 407: | ||
| % 39.43 | | % 39.43 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Eulemur_macaco/all_assembly_versions/GCA_001262655.1_Emacaco_refEf_BWA_oneround/ Black lemur] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Eulemur_macaco/all_assembly_versions/GCA_001262655.1_Emacaco_refEf_BWA_oneround/ Black lemur] | ||
! | ! 21 | ||
! 405987 | ! 405987 | ||
! RecipBest | ! RecipBest | ||
| Line 422: | Line 422: | ||
| % 39.60 | | % 39.60 | ||
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Eulemur_flavifrons/all_assembly_versions/GCA_001262665.1_Eflavifronsk33QCA/ Sclater's lemur] | | [ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Eulemur_flavifrons/all_assembly_versions/GCA_001262665.1_Eflavifronsk33QCA/ Sclater's lemur] | ||
! | ! 52 | ||
! 413352 | ! 413352 | ||
! RecipBest | ! RecipBest | ||
| Line 437: | Line 437: | ||
| % 39.51 | | % 39.51 | ||
| [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAQR03 Bushbaby] | | [http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAQR03 Bushbaby] | ||
! | ! 137 | ||
! 13852661 | ! 13852661 | ||
! SyntenicNet | ! SyntenicNet | ||
Latest revision as of 18:45, 23 October 2017
see also
- Human 27-way Hg38 27-way conservation alignment
- Human 27-way Hg38 27-way 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-preview 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-preview |
chrom count |
total size |
non-N bases |
N base count |
% masked | common name src info |
coverage X |
N50 chrom.sizes |
alignment type | % of hg38 matched (chainLink table) |
chain minScore |
chain linearGap |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | hg38 | 455 | 3,209,286,105 | 3,049,315,783 | 159,970,322 | % 52.10 | Human | 20 | 145138636 | N/A | N/A | 3000 | medium |
| 02 | panTro5 | 44,449 | 3,231,170,666 | 3,132,619,616 | 98,551,050 | % 52.72 | Chimp | 6 | 135926727 | SyntenicNet | 95.355% | 5000 | medium |
| 03 | panPan2 | 10,274 | 3,286,643,896 | 2,725,890,006 | 560,753,890 | % 50.59 | Bonobo | 26 | 144709823 | SyntenicNet | 92.685% | 3000 | medium |
| 04 | gorGor5 | 15,998 | 3,080,431,298 | 3,080,431,298 | 0 | % 50.02 | Gorilla | 71 | 10016017 | SyntenicNet | 94.691% | 3000 | medium |
| 05 | ponAbe2 | 55 | 3,446,771,396 | 3,093,543,172 | 353,228,224 | % 50.89 | Orangutan | 6 | 135191526 | SyntenicNet | 89.187% | 5000 | medium |
| 06 | nomLeu3 | 17,492 | 2,962,077,449 | 2,756,609,047 | 205,468,402 | % 51.14 | Gibbon | 5.6 | 117381234 | SyntenicNet | 86.379% | 3000 | medium |
| 07 | rheMac8 | 284,728 | 3,236,224,332 | 3,142,091,753 | 94,132,579 | % 54.33 | Rhesus | 47.4 | 144306982 | SyntenicNet | 84.506% | 5000 | medium |
| 08 | macFas5 | 7,601 | 2,946,843,737 | 2,803,866,385 | 142,977,352 | % 50.11 | Crab-eating macaque | 68 | 152835861 | SyntenicNet | 85.675% | 3000 | medium |
| 09 | macNem1 | 9,734 | 2,948,720,071 | 2,838,503,040 | 110,217,031 | % 50.07 | Pig-tailed macaque | 113.1 | 15219753 | SyntenicNet | 83.524% | 5000 | medium |
| 10 | cerAty1 | 11,434 | 2,848,262,899 | 2,787,289,385 | 60,973,514 | % 49.92 | Sooty mangabey | 192 | 12849131 | SyntenicNet | 83.847% | 5000 | medium |
| 11 | papAnu3 | 63,251 | 2,948,397,226 | 2,893,266,807 | 55,130,419 | % 52.40 | Baboon | 85 | 139646187 | SyntenicNet | 86.336% | 3000 | medium |
| 12 | chlSab2 | 2,004 | 2,789,656,328 | 2,752,000,999 | 37,655,329 | % 48.77 | Green monkey | 95 | 101219884 | SyntenicNet | 84.393% | 5000 | medium |
| 13 | manLeu1 | 12,822 | 3,062,009,387 | 2,721,424,085 | 340,585,302 | % 49.47 | Drill | 117.2 | 3186748 | SyntenicNet | 82.498% | 5000 | medium |
| 14 | nasLar1 | 319,550 | 3,011,982,740 | 2,397,109,760 | 614,872,980 | % 46.33 | Proboscis monkey | 290 | 137426304 | RecipBest | 74.541% | 3000 | medium |
| 15 | colAng1 | 13,124 | 2,970,124,662 | 2,679,973,136 | 290,151,526 | % 49.72 | Angolan colobus | 86.8 | 7840981 | SyntenicNet | 81.641% | 5000 | medium |
| 16 | rhiRox1 | 135,512 | 2,899,552,139 | 2,856,044,136 | 43,508,003 | % 51.07 | Golden snub-nosed monkey | 53.7 | 1549224 | SyntenicNet | 85.109% | 3000 | medium |
| 17 | rhiBie1 | 105,031 | 2,977,074,741 | 2,801,879,982 | 175,194,759 | % 50.27 | Black snub-nosed monkey | 76.6 | 2225337 | SyntenicNet | 83.065% | 5000 | medium |
| 18 | calJac3 | 14,205 | 2,914,958,544 | 2,752,505,800 | 162,452,744 | % 47.71 | Marmoset | 6 | 132174527 | RecipBest | 71.709% | 3000 | medium |
| 19 | saiBol1 | 2,685 | 2,608,572,064 | 2,477,131,095 | 131,440,969 | % 46.69 | Squirrel monkey | 80 | 18744880 | RecipBest | 70.565% | 3000 | medium |
| 20 | cebCap1 | 7,156 | 2,717,703,182 | 2,610,499,094 | 107,204,088 | % 47.29 | White-faced sapajou | 81 | 5274112 | RecipBest | 70.683% | 5000 | medium |
| 21 | aotNan1 | 28,922 | 2,861,684,817 | 2,714,439,489 | 147,245,328 | % 47.38 | Ma's night monkey | 132.4 | 8268663 | RecipBest | 70.629% | 5000 | medium |
| 22 | tarSyr2 | 337,189 | 3,453,864,774 | 3,405,755,564 | 48,109,210 | % 47.85 | Tarsier | 48 | 401181 | SyntenicNet | 56.022% | 3000 | medium |
| 23 | micMur3 | 7,678 | 2,487,409,138 | 2,386,321,897 | 101,087,241 | % 41.27 | Mouse lemur | 221.6 | 108171978 | RecipBest | 29.728% | 3000 | medium |
| 24 | proCoq1 | 22,539 | 2,798,152,141 | 2,083,764,525 | 714,387,616 | % 39.39 | Coquerel's sifaka | 104.7 | 5604909 | RecipBest | 32.467% | 5000 | medium |
| 25 | eulMac1 | 26,772 | 2,119,875,225 | 2,101,039,320 | 18,835,905 | % 39.43 | Black lemur | 21 | 405987 | RecipBest | 33.708% | 5000 | medium |
| 26 | eulFla1 | 38,366 | 2,115,567,618 | 2,094,103,399 | 21,464,219 | % 39.60 | Sclater's lemur | 52 | 413352 | RecipBest | 33.326% | 5000 | medium |
| 27 | otoGar3 | 7,793 | 2,519,724,550 | 2,359,530,453 | 160,194,097 | % 39.51 | Bushbaby | 137 | 13852661 | SyntenicNet | 53.196% | 3000 | medium |
