| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002195.4/ |
| NCBI Version | Amel_4.5 |
| Source | Assembled chromosomes from RefSeq (GCF_000002195.4): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/ |
| UCSC Assembly | none |
| Local Assembly | amel5 |
| Bowtie Idx | a_mellifera_amel5 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | https://epd.expasy.org/ftp/mga/amel5/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=amel5 |
| Assembly support status | full |
A. carolinensis (May 2010 AnoCar2.0/anoCar2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000090745.1/ |
| NCBI Version | AnoCar2.0 |
| Source | Assembled chromosomes from RefSeq (GCF_000090745.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/090/745/GCF_000090745.1_AnoCar2.0/ |
| UCSC Assembly | anoCar2 |
| Local Assembly | anoCar2 |
| Bowtie Idx | a_carolinensis_anoCar2 |
| liftOver | anoCar2ToHg19, anoCar2ToHg38, anoCar2ToMm10, anoCar2ToMm9, anoCar2ToXenTro9 |
| RepeatMasker | rmsk/rmsk_anoCar2.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/anoCar2/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 |
| Assembly support status | basic |
A. thaliana (Feb 2011 TAIR10/araTha1)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001735.3/ |
| NCBI Version | TAIR10 |
| Source | Assembled chromosomes from RefSeq (GCF_000001735.3): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/ |
| UCSC Assembly | araTha1 |
| Local Assembly | araTha1 |
| Bowtie Idx | a_thaliana_araTha1 |
| liftOver | none |
| RepeatMasker | rmsk/rmsk_araTha1.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/araTha1/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=araTha1 |
| Assembly support status | full |
B. taurus (Aug 2006 Btau_3.1/bosTau3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000003205.1/ |
| NCBI Version | Btau_3.1 |
| Source | Assembled chromosomes from RefSeq (GCF_000003205.1) |
| UCSC Assembly | bosTau3 |
| Local Assembly | bosTau3 |
| Bowtie Idx | b_taurus_bosTau3 |
| liftOver | bosTau3ToHg18, bosTau3ToMm8, bosTau3ToMm9 |
| RepeatMasker | rmsk/rmsk_bosTau3.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau3 |
| Assembly support status | partial |
B. taurus (Nov 2014 Bos_taurus_UMD_3.1.1/bosTau8)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.6/ |
| NCBI Version | Bos_taurus_UMD_3.1.1 |
| Source | Assembled chromosomes from RefSeq (GCF_000003055.6): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/055/GCF_000003055.6_Bos_taurus_UMD_3.1.1/ |
| UCSC Assembly | bosTau8 |
| Local Assembly | bosTau8 |
| Bowtie Idx | b_taurus_bosTau8 |
| liftOver | bosTau8ToHg38, bosTau8ToMm10, bosTau8ToOviAri3 |
| RepeatMasker | rmsk/rmsk_bosTau8.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau8 |
| Assembly support status | partial |
C. familiaris (May 2005 CanFam2.0/canFam2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.2/ |
| NCBI Version | CanFam2.0 |
| Source | Assembled chromosomes from Refseq (GCF_000002285.2) |
| UCSC Assembly | canFam2 |
| Local Assembly | canFam2 |
| Bowtie Idx | d_rerio_canFam2 |
| liftOver | canFam2ToCanFam3, canFam2ToHg18, canFam2ToHg19, canFam2ToMm9 |
| RepeatMasker | rmsk/rmsk_canFam2.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=canFam2 |
| Assembly support status | partial |
C. familiaris (Sep 2011 CanFam3.1/canFam3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.3/ |
| NCBI Version | CanFam3.1 |
| Source | Assembled chromosomes from Refseq (GCF_000002285.3): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/ |
| UCSC Assembly | canFam3 |
| Local Assembly | canFam3 |
| Bowtie Idx | d_rerio_canFam3 |
| liftOver | canFam3ToCanFam2, canFam3ToHg19, canFam3ToHg38, canFam3ToMm10, canFam3ToMm9, canFam3ToRn6, canFam3ToXenTro9, canFam3ToMm39 |
| RepeatMasker | rmsk/rmsk_canFam3.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/canFam3/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=canFam3 |
| Assembly support status | full |
C. porcellus (Feb 2008 Cavpor3.0/cavPor3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000151735.1/ |
| NCBI Version | Cavpor3.0 |
| Source | Assembled chromosomes from Refseq (GCF_000151735.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/151/735/GCF_000151735.1_Cavpor3.0/ |
| UCSC Assembly | cavPor3 |
| Local Assembly | cavPor3 |
| Bowtie Idx | c_porcellus_cavPor3 |
| liftOver | cavPor3ToHg18, cavPor3ToHg19, cavPor3ToHg38, cavPor3ToMm10, cavPor3ToMm9, cavPor3ToRn6, cavPor3ToMm39 |
| RepeatMasker | rmsk/rmsk_cavPor3.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/cavPor3/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=cavPor3 |
| Assembly support status | basic |
C. elegans (Oct 2010 WBcel215/ce10)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.5/ |
| NCBI Version | WBcel215 |
| Source | Assembled chromosomes from Genbank (GCA_000002985.2): https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/invertebrates/Caenorhabditis_elegans/WBcel215/ |
| UCSC Assembly | ce10 |
| Local Assembly | ce10 |
| Bowtie Idx | c_elegans_ce10 |
| liftOver | ce10ToCe4, ce10ToCe6 |
| RepeatMasker | rmsk/rmsk_ce10.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/ce10/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce10 |
| Assembly support status | full |
C. elegans (Feb 2013 WBcel235/ce11)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/ |
| NCBI Version | WBcel235 |
| Source | Assembled chromosomes from RefSeq (GCF_000002985.6): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/ |
| UCSC Assembly | ce11 |
| Local Assembly | ce11 |
| Bowtie Idx | c_elegans_ce11 |
| liftOver | ce11ToCe10, ce11ToCe6 |
| RepeatMasker | rmsk/rmsk_ce11.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce11 |
| Assembly support status | partial |
C. elegans (Jan 2007 WS170/ce4)
| NCBI Assembly | none |
| NCBI Version | WS170 |
| Source | Assembled chromosomes from RefSeq (suppressed) |
| UCSC Assembly | ce4 |
| Local Assembly | ce4 |
| Bowtie Idx | c_elegans_ce4 |
| liftOver | ce4ToCe6, ce4ToCe10 |
| RepeatMasker | rmsk/rmsk_ce4.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce4 |
| Assembly support status | partial |
C. elegans (May 2008 WS190/ce6)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.1/ |
| NCBI Version | WS190 |
| Source | Assembled chromosomes from RefSeq (GCF_000002985.1_WS190): https://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Caenorhabditis_elegans/all_assembly_versions/GCF_000002985.1_WS190/ |
| UCSC Assembly | ce6 |
| Local Assembly | ce6 |
| Bowtie Idx | c_elegans_ce6 |
| liftOver | ce6ToCe4, ce6ToCe10 |
| RepeatMasker | rmsk/rmsk_ce6.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/ce6/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=ce6 |
| Assembly support status | partial |
C. intestinalis (Sep 2017 Kyoto KH/ci4)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000224145.3/ |
| NCBI Version | Kyoto KH |
| Source | Assembled chromosomes from Refseq (GCF_000224145.3): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/145/GCF_000224145.3_KH/ |
| UCSC Assembly | none |
| Local Assembly | ci4 |
| Bowtie Idx | c_intestinalis_ci4 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | none |
| Assembly support status | basic |
D. rerio (Sep 2014 GRCz10/danRer10)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/ |
| NCBI Version | GRCz10 |
| Source | Assembled chromosomes from Refseq (GCF_000002035.5): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.5_GRCz10/ |
| UCSC Assembly | danRer10 |
| Local Assembly | danRer10 |
| Bowtie Idx | d_rerio_danRer10 |
| liftOver | danRer10ToHg38, danRer10ToHg19, danRer10ToMm10, danRer10ToDanRer7, danRer10ToRn6, danRer10ToGalGal5 |
| RepeatMasker | rmsk/rmsk_danRer10.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7 |
| Assembly support status | partial |
D. rerio (July 2010 Zv9/danRer7)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.4/ |
| NCBI Version | Zv9 |
| Source | Assembled chromosomes from Refseq (GCF_000002035.4): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.4_Zv9/ |
| UCSC Assembly | danRer7 |
| Local Assembly | danRer7 |
| Bowtie Idx | d_rerio_danRer7 |
| liftOver | danRer7ToHg19, danRer7ToMm9, danRer7ToMm10 |
| RepeatMasker | rmsk/rmsk_danRer7.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/danRer7/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=danRer7 |
| Assembly support status | full |
D. melanogaster (Apr 2006 BDGP R5/dm3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/ |
| NCBI Version | Release 5 (R5) |
| Source | Assembled chromosomes from Refseq (RELEASE_5): https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Drosophila_melanogaster/RELEASE_5/ |
| UCSC Assembly | dm3 |
| Local Assembly | dm3 |
| Bowtie Idx | d_melanogaster_dm3 |
| liftOver | dm3ToDm6 |
| RepeatMasker | rmsk/rmsk_dm3.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/dm3/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3 |
| Assembly support status | full |
D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/ |
| NCBI Version | Release 6 plus ISO1 MT |
| Source | Assembled chromosomes from Refseq (GCF_000001215.4): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT |
| UCSC Assembly | dm6 |
| Local Assembly | dm6 |
| Bowtie Idx | d_melanogaster_dm6 |
| liftOver | dm6ToDm3 |
| RepeatMasker | rmsk/rmsk_dm6.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/dm6/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=dm6 |
| Assembly support status | full |
D. pulex (Sep 2019 PA42 4.1/dpu2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCA_900092285.2 |
| NCBI Version | PA42 4.1 |
| Source | Scaffolds from GenBank (GCA_900092285.2) |
| UCSC Assembly | none |
| Local Assembly | dpu2 |
| Bowtie Idx | d_pulex_dpu2 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | https://epd.expasy.org/ftp/mga/dpu2/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=dpu2 |
| Assembly support status | full |
G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.4/ |
| NCBI Version | Gallus_gallus-5.0 |
| Source | Assembled chromosomes from RefSeq (GCF_000002315.4): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/315/GCF_000002315.4_Gallus_gallus-5.0/ |
| UCSC Assembly | galGal5 |
| Local Assembly | galGal5 |
| Bowtie Idx | g_gallus_galGal5 |
| liftOver | galGal5ToDanRer10, galGal5ToHg38, galGal5ToMm10, galGal5ToRn6, galGal5ToXenTro9 |
| RepeatMasker | rmsk/rmsk_galGal5.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/galGal5/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=galGal5 |
| Assembly support status | full |
H. sapiens (March 2006 NCBI36/hg18)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.12/ |
| NCBI Version | NCBI36 |
| Source | Assembled chromosomes from RefSeq: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.2/ |
| UCSC Assembly | hg18 |
| Local Assembly | hg18 |
| Bowtie Idx | h_sapiens_hg18 |
| liftOver | hg18ToHg19, hg18ToHg38, hg18ToMm8, hg18ToMm9, hg18ToBosTau3, hg18ToCanFam2, hg18ToPanTro2 |
| RepeatMasker | rmsk/rmsk_hg18.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/hg18/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18 |
| Assembly support status | full |
H. sapiens (Feb 2009 GRCh37/hg19)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ |
| NCBI Version | GRCh37 |
| Source | Assembled chromosomes from RefSeq (GCF_000001405.13): https://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.1/ |
| UCSC Assembly | hg19 |
| Local Assembly | hg19 |
| Bowtie Idx | h_sapiens_hg19 |
| liftOver | hg19ToHg18, hg19ToHg38, hg19ToMm9, hg19ToMm10, hg19ToHg19a, hg19ToCanFam2, hg19ToCanFam3, hg19ToDanRer7, hg19ToDanRer10, hg19ToOviAri3, hg19ToPanTro2, hg19ToRn5, hg19ToRn6, hg19ToSusScr3, hg19ToRheMac8, hg19ToRheMac10 |
| RepeatMasker | rmsk/rmsk_hg19.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/hg19/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=hg19 |
| Assembly support status | full |
H. sapiens (Feb 2009 Alternate GRCh37/hg19a)
| NCBI Assembly | none |
| NCBI Version | none |
| Source | hg19 alternate assembly |
| UCSC Assembly | none |
| Local Assembly | hg19a |
| Bowtie Idx | h_sapiens_hg19a |
| liftOver | hg19aToHg19 |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | none |
| Assembly support status | basic |
H. sapiens (Dec 2013 GRCh38/hg38)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/ |
| NCBI Version | GRCh38 |
| Source | Assembled chromosomes from RefSeq (GCF_000001405.26): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/ |
| UCSC Assembly | hg38 |
| Local Assembly | hg38 |
| Bowtie Idx | h_sapiens_hg38 |
| liftOver | hg38ToHg19, hg38ToMm10, hg38ToBosTau8, hg38ToCanFam3, hg38ToDanRer10, hg38ToGalGal5, hg38ToOviAri3, hg38ToPanTro5, hg38ToRn5, hg38ToRn6, hg38ToSusScr3, hg38ToRheMac8, hg38ToMm39 |
| RepeatMasker | rmsk/rmsk_hg38.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=hg38 |
| Assembly support status | full |
H. sapiens (May 2013 humanSTF500)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/'>https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/ |
| NCBI Version | GRCh38 |
| Source |
Assembled chromosomes from RefSeq (GCF_000001405.26): |
| UCSC Assembly | humanSTF500 |
| Local Assembly | humanSTF500 |
| Bowtie Idx | humanSTF500 |
| liftOver | none |
| RepeatMasker | rmsk/rmsk_humanSTF500.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/humanSTF500/ |
| UCSC Genome Browser | http://vader.wistar.upenn.edu/cgi-bin/hgTracks?db=humanSTF500 |
| Assembly support status | partial |
M. musculus (March 2012 GRCm38/mm10)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ |
| NCBI Version | GRCm38 |
| Source | Assembled chromosomes from RefSeq (GCF_000001635.20): https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.38.1/ |
| UCSC Assembly | mm10 |
| Local Assembly | mm10 |
| Bowtie Idx | m_musculus_mm10 |
| liftOver | mm10ToMm9, mm10ToHg19, mm10ToHg38, mm10ToBosTau8, mm10ToCanFam3, mm10ToGalGal5, mm10ToDanRer10, mm10ToDanRer7, mm10ToOviAri3, mm10ToOreNil2, mm10ToPanTro5, mm10ToRn5, mm10ToRn6, mm10ToSusScr3, mm10ToRheMac8, mm10ToMm39 |
| RepeatMasker | rmsk/rmsk_mm10.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/mm10/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=mm10 |
| Assembly support status | full |
M. musculus (June 2020 GRCm39/mm39)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/ |
| NCBI Version | GRCm39 |
| Source | https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/reference/GCF_000001635.27_GRCm39/ |
| UCSC Assembly | mm39 |
| Local Assembly | mm39 |
| Bowtie Idx | m_musculus_mm39 |
| liftOver | mm39ToCanFam3, mm39ToCavPor3, mm39ToHg38, mm39ToMm10, mm39ToMm9, mm39ToRheMac10, mm39ToRn6, mm39ToSusScr3, mm39ToXenTro9 |
| RepeatMasker | rmsk/rmsk_mm39.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/mm39/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=mm39 |
| Assembly support status | full |
M. musculus (Feb 2006 NCBI36/mm8)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.15/ |
| NCBI Version | NCBI36 (MGSCv36) |
| Source | Assembled chromosomes from RefSeq (GCF_000001635.15): https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.36.1/ |
| UCSC Assembly | mm8 |
| Local Assembly | mm8 |
| Bowtie Idx | none |
| liftOver | mm8ToMm9, mm8ToHg18 |
| RepeatMasker | rmsk/rmsk_mm8.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8 |
| Assembly support status | partial |
M. musculus (July 2007 NCBI37/mm9)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.18/ |
| NCBI Version | NCBI37 (MGSCv37) |
| Source | Assembled chromosomes from RefSeq (GCF_000001635.18): https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.37.1/ |
| UCSC Assembly | mm9 |
| Local Assembly | mm9 |
| Bowtie Idx | m_musculus_mm9 |
| liftOver | mm9ToMm8, mm9ToMm10, mm9ToHg18, mm9ToHg19, mm9ToBosTau3, mm9ToCanFam2, mm9ToDanRer7, mm9ToPanTro2, mm9ToRn5, mm9ToMm39 |
| RepeatMasker | rmsk/rmsk_mm9.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/mm9/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=mm9 |
| Assembly support status | full |
O. niloticus (Feb 2012 Orenil1.1/oreNil2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000188235.2/ |
| NCBI Version | Orenil1.1 |
| Source | Assembled chromosomes from Refseq (GCF_000188235.2): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/235/GCF_000188235.2_Orenil1.1/ |
| UCSC Assembly | oreNil2 |
| Local Assembly | oreNil2 |
| Bowtie Idx | o_niloticus_oreNil2 |
| liftOver | oreNil2ToMm10 |
| RepeatMasker | rmsk/rmsk_oreNil2.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=oreNil2 |
| Assembly support status | partial |
O. niloticus (Jun 2018 O_niloticus_UMD_NMBU/oreNil3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_001858045.2/ |
| NCBI Version | O_niloticus_UMD_NMBU |
| Source | Assembled chromosomes from Refseq (GCF_001858045.2): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/858/045/GCF_001858045.2_O_niloticus_UMD_NMBU/ |
| UCSC Assembly | none |
| Local Assembly | oreNil3 |
| Bowtie Idx | o_niloticus_oreNil3 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | none |
| Assembly support status | basic |
O. latipes (May 2007 ASM31367v1/oryLat)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000313675.1/ |
| NCBI Version | ASM276v1 |
| Source | Assembled chromosomes from Refseq (GCF_000313675.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/313/675/GCF_000313675.1_ASM31367v1/GCF_000313675.1_ASM31367v1_assembly_structure/ |
| UCSC Assembly | none |
| Local Assembly | oryLat |
| Bowtie Idx | o_latipes_oryLat |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | none |
| Assembly support status | basic |
O. sativa Japonica (Oct 2015 IRGSP-1.0/orySatJ)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_001433935.1/ |
| NCBI Version | IRGSP-1.0 |
| Source | Assembled chromosomes from Refseq (GCF_001433935.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/433/935/GCF_001433935.1_IRGSP-1.0/ |
| UCSC Assembly | none |
| Local Assembly | orySatJ |
| Bowtie Idx | o_sativa_japonica_orySatJ |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | none |
| Assembly support status | basic |
O. aries (Aug 2012 ISGC Oar_v3.1/oviAri3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.1/ |
| NCBI Version | Oar_v3.1 |
| Source | Assembled chromosomes from GenBank (GCF_000298735.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/298/735/GCA_000298735.1_Oar_v3.1/ |
| UCSC Assembly | oviAri3 |
| Local Assembly | oviAri3 |
| Bowtie Idx | o_aries_oviAri3 |
| liftOver | oviAri3ToBosTau8, oviAri3ToHg19, oviAri3ToHg38, oviAri3ToMm10, oviAri3ToOviAri4, oviAri3ToSusScr3 |
| RepeatMasker | rmsk/rmsk_oviAri3.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/oviAri3/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=oviAri3 |
| Assembly support status | partial |
O. aries (Nov 2015 Oar_v4.0/oviAri4)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2/ |
| NCBI Version | Oar_v4.1 |
| Source | Assembled chromosomes from GenBank (GCF_000298735.2): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/298/735/GCA_000298735.2_Oar_v4.0 |
| UCSC Assembly | oviAri4 |
| Local Assembly | oviAri4 |
| Bowtie Idx | o_aries_oviAri4 |
| liftOver | none |
| RepeatMasker | rmsk/rmsk_oviAri4.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/oviAri4/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=oviAri4 |
| Assembly support status | none |
P. troglodytes (Mar 2006 Pan_troglodytes-2.1/panTro2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.3/ |
| NCBI Version | Pan_troglodytes-2.1 |
| Source | Assembled chromosomes from Refseq (GCF_000001515.3) |
| UCSC Assembly | panTro2 |
| Local Assembly | panTro2 |
| Bowtie Idx | p_troglodytes_panTro2 |
| liftOver | panTro2ToHg18, panTro2ToHg19, panTro2ToMm8, panTro2ToMm9, panTro2ToCanFam2 |
| RepeatMasker | rmsk/rmsk_panTro2.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=panTro2 |
| Assembly support status | partial |
P. troglodytes (May 2016 Pan_tro3.0/panTro5)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.7/ |
| NCBI Version | Pan_tro3.0 |
| Source | Assembled chromosomes from Refseq (GCF_000001515.7): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/515/GCF_000001515.7_Pan_tro_3.0/GCF_000001515.7_Pan_tro_3.0_assembly_structure/ |
| UCSC Assembly | panTro5 |
| Local Assembly | panTro5 |
| Bowtie Idx | p_troglodytes_panTro5 |
| liftOver | panTro5ToHg38, panTro5ToMm10, panTro5ToRheMac8, panTro5ToRn6 |
| RepeatMasker | rmsk/rmsk_panTro5.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=panTro5 |
| Assembly support status | partial |
P. falciparum (Apr 2016 ASM276v2/pfa2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002765.4/ |
| NCBI Version | ASM276v2 |
| Source | Assembled chromosomes from Refseq (GCF_000002765.4) |
| UCSC Assembly | none |
| Local Assembly | pfa2 |
| Bowtie Idx | p_falciparum_pfa2 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | https://epd.expasy.org/ftp/mga/pfa2/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=pfa2 |
| Assembly support status | full |
P. falciparum (Oct 2007 ASM276v1/plasFalc1)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002765.3/ |
| NCBI Version | ASM276v1 |
| Source | Assembled chromosomes from Refseq (GCF_000002765.3) |
| UCSC Assembly | plasFalc1 |
| Local Assembly | plasFalc1 |
| Bowtie Idx | p_falciparum_plasFalc1 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | none |
| UCSC Genome Browser | http://microbes.ucsc.edu/cgi-bin/hgTracks?db=plasFalc1 |
| Assembly support status | basic |
M. mulatta (Feb 2019 Mmul_10/rheMac10)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_003339765.1/ |
| NCBI Version | Mmul_10 |
| Source | Assembled chromosomes from RefSeq (GCF_003339765.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/339/765/GCF_003339765.1_Mmul_10/ |
| UCSC Assembly | rheMac10 |
| Local Assembly | rheMac10 |
| Bowtie Idx | m_mulatta_rheMac10 |
| liftOver | rheMac10ToHg19, rheMac10ToHg38, rheMac10ToMm10, rheMac10ToRheMac8, rheMac10ToMm39 |
| RepeatMasker | rmsk/rmsk_rheMac10.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/rheMac10/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=rheMac10 |
| Assembly support status | partial |
M. mulatta (Nov 2015 BCM Mmul_8.0.1/rheMac8)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000772875.2/ |
| NCBI Version | Mmul_8.0.1 |
| Source | Assembled chromosomes from RefSeq (GCF_000772875.2): https://ftp.ncbi.nlm.nih.gov/genomes/Macaca_mulatta/Assembled_chromosomes |
| UCSC Assembly | rheMac8 |
| Local Assembly | rheMac8 |
| Bowtie Idx | m_mulatta_rheMac8 |
| liftOver | rheMac8ToHg19, rheMac8ToHg38, rheMac8ToMm10, rheMac8ToPanTro5, rheMac8ToRn6 |
| RepeatMasker | rmsk/rmsk_rheMac8.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/rheMac8/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=rheMac8 |
| Assembly support status | full |
R. norvegicus (Mar 2012 Rnor_5.0/rn5)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.4/ |
| NCBI Version | Rnor_5.0 |
| Source | Assembled chromosomes from RefSeq (GCF_000001895.4): https://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ARCHIVE/BUILD.5.1 |
| UCSC Assembly | rn5 |
| Local Assembly | rn5 |
| Bowtie Idx | r_norvegicus_rn5 |
| liftOver | rn5ToMm9, rn5ToMm10, rn5ToHg19, rn5ToHg38, rn5ToDanRer7, rn5ToRn6 |
| RepeatMasker | rmsk/rmsk_rn5.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=rn5 |
| Assembly support status | partial |
R. norvegicus (Jul 2014 Rnor_6.0/rn6)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCA_000001895.4/ |
| NCBI Version | Rnor_6.0 |
| Source | Assembled chromosomes from RefSeq (GCF_000001895.4): https://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ARCHIVE/BUILD.5.1 |
| UCSC Assembly | rn6 |
| Local Assembly | rn6 |
| Bowtie Idx | r_norvegicus_rn6 |
| liftOver | rn6ToRn5, rn6ToHg19, rn6ToHg38, rn6ToMm10, rn6ToBosTau8, rn6ToCanFam3, rn6ToPanTro5, rn6ToDanRer10, rn6ToGalGal5, rn6ToRheMac8, rn6ToMm39 |
| RepeatMasker | rmsk/rmsk_rn6.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/rn6/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=rn6 |
| Assembly support status | full |
S. cerevisiae (June 2008 NCBI2.1/sacCer2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/bioproject/128/ |
| NCBI Version | NCBI2.1 |
| Source | Assembled chromosomes from RefSeq |
| UCSC Assembly | sacCer2 |
| Local Assembly | sacCer2 |
| Bowtie Idx | s_cerevisiae_sacCer2 |
| liftOver | sacCer2ToSacCer3 |
| RepeatMasker | rmsk/rmsk_sacCer2.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=sacCer2 |
| Assembly support status | partial |
S. cerevisiae (Apr 2011 R64/sacCer3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/ |
| NCBI Version | R64 |
| Source | Assembled chromosomes from RefSeq (GCF_000146045.2): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/ |
| UCSC Assembly | sacCer3 |
| Local Assembly | sacCer3 |
| Bowtie Idx | s_cerevisiae_sacCer3 |
| liftOver | sacCer3ToSacCer2 |
| RepeatMasker | rmsk/rmsk_sacCer3.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/sacCer3 |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=sacCer3 |
| Assembly support status | full |
S. pombe (Aug 2015 ASM294v2/spo2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002945.1/ |
| NCBI Version | ASM294v2 |
| Source | Assembled chromosomes from RefSeq (GCF_000002945.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/945/GCF_000002945.1_ASM294v2/ |
| UCSC Assembly | none |
| Local Assembly | spo2 |
| Bowtie Idx | s_cerevisiae_sacCer3 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | https://epd.expasy.org/ftp/mga/spo2/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=spo2 |
| Assembly support status | full |
S. scrofa (Aug 2011 Sscrofa10.2/susScr3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.5/ |
| NCBI Version | Sscrofa10.2 |
| Source | Assembled chromosomes from Refseq (GCF_000003025.5): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.5_Sscrofa10.2/ |
| UCSC Assembly | susScr3 |
| Local Assembly | susScr3 |
| Bowtie Idx | s_scrofa_susScr3 |
| liftOver | susScr3ToHg19, susScr3ToHg38, susScr3ToMm10, susScr3ToOviAri3, susScr3ToMm39 |
| RepeatMasker | rmsk/rmsk_susScr3.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=susScr3 |
| Assembly support status | partial |
X. laevis (Aug 2016 Xenopus_laevis_v2/xenLae2)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_001663975.1/ |
| NCBI Version | Xenopus_laevis_v2 |
| Source | Assembled chromosomes from Refseq (GCF_001663975.1): https://ftp.ncbi.nlm.nih.gov/genomes/Xenopus_laevis/Assembled_chromosomes/seq/ |
| UCSC Assembly | xenLae2 |
| Local Assembly | xenLae2 |
| Bowtie Idx | x_laevis_xenLae2 |
| liftOver | xenLae2ToHg38, xenLae2ToMm10, xenLae2ToXenTro9 |
| RepeatMasker | rmsk/rmsk_xenLae2.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/xenLae2/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=xenLae |
| Assembly support status | basic |
X. tropicalis (Nov 2009 v4.2/xenTro3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.1/ |
| NCBI Version | v4.2 |
| Source | Assembled chromosomes from Refseq (GCF_000004195.1) |
| UCSC Assembly | xenTro3 |
| Local Assembly | xenTro3 |
| Bowtie Idx | x_tropicalis_xenTro3 |
| liftOver | xenTro3ToHg19, xenTro3ToMm10, xenTro3ToMm9, xenTro3ToDanRer7 |
| RepeatMasker | rmsk/rmsk_xenTro3.SGA.gz |
| MGA FTP | none |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=xenTro3 |
| Assembly support status | partial |
X. tropicalis (Jul 2016 Xenopus_tropicalis_v9.1/xenTro9)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.3/ |
| NCBI Version | Xenopus_tropicalis_v9.1 |
| Source | Assembled chromosomes from Refseq (GCF_000004195.3): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/195/GCF_000004195.3_Xenopus_tropicalis_v9.1/ |
| UCSC Assembly | xenTro9 |
| Local Assembly | xenTro9 |
| Bowtie Idx | x_tropicalis_xenTro9 |
| liftOver | xenTro9ToCanFam3, xenTro9ToHg38, xenTro9ToMm10, xenTro9ToXenLae2, xenTro9ToXenTro3, xenTro9ToMm39 |
| RepeatMasker | rmsk/rmsk_xenTro9.SGA.gz |
| MGA FTP | https://epd.expasy.org/ftp/mga/xenTro9/ |
| UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTracks?db=xenTro9 |
| Assembly support status | partial |
Z. mays (Oct 2013 B73 RefGen_v3/zm3)
| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly/GCF_000005005.1/ |
| NCBI Version | B73 RefGen_v3 |
| Source | Assembled chromosomes from RefSeq (GCF_000005005.1): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/005/GCF_000005005.1_B73_RefGen_v3/ |
| UCSC Assembly | none (zeaMay_b73) |
| Local Assembly | zm3 |
| Bowtie Idx | z_mays_zm3 |
| liftOver | none |
| RepeatMasker | none |
| MGA FTP | https://epd.expasy.org/ftp/mga/zm3/ |
| UCSC Genome Browser | https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt&genome=zm3 |
| Assembly support status | full |