> ## Documentation Index
> Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt
> Use this file to discover all available pages before exploring further.
# IGV Hosted Reference Genomes
> The IGV browser comes with many hosted options for common Reference Genomes to view Alignment Files to.
Here is a list of the options provided:
| Id | Reference Name | Fasta URL | Index URL | Supplementary Tracks |
| ---------------- | ------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------- |
| chm13v2.0 | Human (T2T CHM13-v2.0) | [chm13v2.0.fa](https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa) | [chm13v2.0.fa.fai](https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa.fai) | CAT/Liftoff Genes, Augustus, Genes |
| chm13v1.1 | Human (T2T CHM13-v1.1) | [GCA\_009914755.3\_CHM13\_T2T\_v1.1\_genomic.fna](https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna) | [GCA\_009914755.3\_CHM13\_T2T\_v1.1\_genomic.fna.fai](https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna.fai) | Annotations, Genes |
| hg38 | Human (GRCh38/hg38) | [hg38.fa](https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa) | [hg38.fa.fai](https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai) | Refseq Genes |
| hg38\_1kg | Human (hg38 1kg/GATK) | [GRCh38\_full\_analysis\_set\_plus\_decoy\_hla.fa](https://1000genomes.s3.amazonaws.com/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa) | [GRCh38\_full\_analysis\_set\_plus\_decoy\_hla.fa.fai](https://1000genomes.s3.amazonaws.com/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai) | Refseq Genes |
| hg19 | Human (GRCh37/hg19) | [hg19.fasta](https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta) | [hg19.fasta.fai](https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta.fai) | Refseq Genes |
| hg18 | Human (hg18) | [hg18.fasta](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta) | [hg18.fasta.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta.fai) | Refseq Genes |
| mm39 | Mouse (GRCm39/mm39) | [mm39.fa](https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa) | [mm39.fa.fai](https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa.fai) | Refseq Genes |
| mm10 | Mouse (GRCm38/mm10) | [mm10.fa](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa) | [mm10.fa.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa.fai) | Refseq Genes |
| mm9 | Mouse (NCBI37/mm9) | [mm9.fasta](https://s3.amazonaws.com/igv.org.genomes/mm9/mm9.fasta) | [mm9.fasta.fai](https://s3.amazonaws.com/igv.org.genomes/mm9/mm9.fasta.fai) | Refseq Genes, Genes |
| rn7 | Rat (rn7) | [rn7.fa](https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa) | [rn7.fa.fai](https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa.fai) | Genes, Genes |
| rn6 | Rat (RGCS 6.0/rn6) | [rn6.fa](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/rn6/rn6.fa) | [rn6.fa.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/rn6/rn6.fa.fai) | Refseq Genes, Genes |
| gorGor6 | Gorilla (Kamilah\_GGO\_v0/gorGor6) | [gorGor6.fa](https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa) | [gorGor6.fa.fai](https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa.fai) | Refseq Genes, Genes |
| gorGor4 | Gorilla (gorGor4.1/gorGor4) | [gorGor4.fa](https://s3.amazonaws.com/igv.org.genomes/gorGor4/gorGor4.fa) | [gorGor4.fa.fai](https://s3.amazonaws.com/igv.org.genomes/gorGor4/gorGor4.fa.fai) | Refseq Genes |
| panTro6 | Chimp (panTro6) (panTro6) | [panTro6.fa](https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa) | [panTro6.fa.fai](https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa.fai) | Refseq Genes, Genes |
| panTro5 | Chimp (panTro5) (panTro5) | [panTro5.fa](https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.fa) | [panTro5.fa.fai](https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.fa.fai) | Refseq Genes, Genes |
| panTro4 | Chimp (SAC 2.1.4/panTro4) | [panTro4.fa](https://s3.amazonaws.com/igv.org.genomes/panTro4/panTro4.fa) | [panTro4.fa.fai](https://s3.amazonaws.com/igv.org.genomes/panTro4/panTro4.fa.fai) | Refseq Genes, Genes |
| macFas5 | Macaca fascicularis (macFas5) | [macFas5.fa](https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa) | [macFas5.fa.fai](https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa.fai) | Genes, Genes |
| GCA\_011100615.1 | Macaca fascicularis 6.0 (GCA\_011100615.1) | [Macaca\_fascicularis.Macaca\_fascicularis\_6.0.dna.toplevel.fa.gz](https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz) | [Macaca\_fascicularis.Macaca\_fascicularis\_6.0.dna.toplevel.fa.gz.fai](https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz.fai) | Annotations, Genes |
| panPan2 | Bonobo (MPI-EVA panpan1.1/panPan2) | [panPan2.fa](https://s3.amazonaws.com/igv.org.genomes/panPan2/panPan2.fa) | [panPan2.fa.fai](https://s3.amazonaws.com/igv.org.genomes/panPan2/panPan2.fa.fai) | Refseq Genes, Genes |
| canFam3 | Dog (Broad CanFam3.1/canFam3) | [canFam3.fa](https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa) | [canFam3.fa.fai](https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa.fai) | Refseq Genes, Genes |
| canFam4 | Dog (UU\_Cfam\_GSD\_1.0/canFam4) | [canFam4.fa](https://s3.amazonaws.com/igv.org.genomes/canFam4/canFam4.fa) | [canFam4.fa.fai](https://s3.amazonaws.com/igv.org.genomes/canFam4/canFam4.fa.fai) | Genes |
| canFam5 | Dog (canFam5) | [canFam5.fa](https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa) | [canFam5.fa.fai](https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa.fai) | Genes, Genes |
| bosTau9 | Cow (ARS-UCD1.2/bosTau9) | [bosTau9.fa](https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa) | [bosTau9.fa.fai](https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa.fai) | Refseq Genes, Genes |
| bosTau8 | Cow (UMD\_3.1.1/bosTau8) | [bosTau8.fa](https://s3.amazonaws.com/igv.org.genomes/bosTau8/bosTau8.fa) | [bosTau8.fa.fai](https://s3.amazonaws.com/igv.org.genomes/bosTau8/bosTau8.fa.fai) | Refseq Genes, Genes |
| susScr11 | Pig (SGSC Sscrofa11.1/susScr11) | [susScr11.fa](https://s3.amazonaws.com/igv.org.genomes/susScr11/susScr11.fa) | [susScr11.fa.fai](https://s3.amazonaws.com/igv.org.genomes/susScr11/susScr11.fa.fai) | Refseq Genes, Genes |
| galGal6 | Chicken (galGal6) | [galGal6.fa](https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa) | [galGal6.fa.fai](https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa.fai) | NCBI Refseq Genes |
| GCF\_016699485.2 | Gallus gallus (GCF\_016699485.2) | [GCF\_016699485.2.fa](https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2.fa) | [GCF\_016699485.2.fa.fai](https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2.fa.fai) | Genes, RefSeq Transcripts |
| danRer11 | Zebrafish (GRCZ11/danRer11) | [danRer11.fa](https://s3.amazonaws.com/igv.org.genomes/danRer11/danRer11.fa) | [danRer11.fa.fai](https://s3.amazonaws.com/igv.org.genomes/danRer11/danRer11.fa.fai) | Refseq Genes, Genes |
| danRer10 | Zebrafish (GRCZ10/danRer10) | [danRer10.fa](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/danRer10/danRer10.fa) | [danRer10.fa.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/danRer10/danRer10.fa.fai) | Refseq Genes, Genes |
| ce11 | C. elegans (ce11) | [ce11.fa](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa) | [ce11.fa.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai) | Refseq Genes |
| dm6 | D. melanogaster (dm6) | [dm6.fa](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa) | [dm6.fa.fai](https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa.fai) | Refseq Genes |
| dm3 | D. melanogaster (dm3) | [dm3.fa](https://s3.amazonaws.com/igv.org.genomes/dm3/dm3.fa) | [dm3.fa.fai](https://s3.amazonaws.com/igv.org.genomes/dm3/dm3.fa.fai) | UCSC Refseq Genes |
| dmel\_r5.9 | D. melanogaster (dmel\_r5.9) | [dmel-all-chromosome-r5.9.fasta](https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel-all-chromosome-r5.9.fasta) | [dmel-all-chromosome-r5.9.fasta.fai](https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel-all-chromosome-r5.9.fasta.fai) | Transcripts |
| sacCer3 | S. cerevisiae (sacCer3) | [sacCer3.fa](https://s3.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa) | [sacCer3.fa.fai](https://s3.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa.fai) | Refseq Genes |
| ASM294v2 | S. pombe (ASM294v2) | [Schizosaccharomyces\_pombe\_all\_chromosomes.fa](https://s3.amazonaws.com/igv.org.genomes/ASM294v2/Schizosaccharomyces_pombe_all_chromosomes.fa) | [Schizosaccharomyces\_pombe\_all\_chromosomes.fa.fai](https://s3.amazonaws.com/igv.org.genomes/ASM294v2/Schizosaccharomyces_pombe_all_chromosomes.fa.fai) | Pombase forward strand, Pombase reverse strand |
| ASM985889v3 | Sars-CoV-2 (ASM985889v3) | [GCF\_009858895.2\_ASM985889v3\_genomic.fna](https://s3.amazonaws.com/igv.org.genomes/ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna) | [GCF\_009858895.2\_ASM985889v3\_genomic.fna.fai](https://s3.amazonaws.com/igv.org.genomes/ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai) | Annotations |
| tair10 | A. thaliana (TAIR 10) | [TAIR10\_chr\_all.fas](https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas) | [TAIR10\_chr\_all.fas.fai](https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas.fai) | Genes |
| GCA\_003086295.2 | Peanut (GCA\_003086295.2) | [GCF\_003086295.2\_arahy.Tifrunner.gnm1.KYV3\_genomic.fna](https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna) | [GCF\_003086295.2\_arahy.Tifrunner.gnm1.KYV3\_genomic.fna.fai](https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna.fai) | Annotations |
| GCF\_001433935.1 | O. sativa IRGSP-1.0 (GCF\_001433935.1) | [GCF\_001433935.1\_IRGSP-1.0\_genomic.fna.gz](https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz) | [GCF\_001433935.1\_IRGSP-1.0\_genomic.fna.gz.fai](https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz.fai) | MSU V7 genes |
| NC\_016856.1 | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S | [NC\_016856.1.fna](https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1.fna) | [NC\_016856.1.fna.fai](https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1.fna.fai) | NC\_016856.1.gff.gz |
| GCA\_000182895.1 | Coprinopsis cinerea okayama7#130 (GCA\_000182895.1) | [GCA\_000182895.1.fa](https://igv-genepattern-org.s3.amazonaws.com/genomes/GCA_000182895.1/GCA_000182895.1.fa) | [GCA\_000182895.1.fa.fai](https://igv-genepattern-org.s3.amazonaws.com/genomes/GCA_000182895.1/GCA_000182895.1.fa.fai) | Gene models |
More info about these options can be found [here](https://github.com/igvteam/igv.js/wiki/Reference-Genome).
To update the reference genome within the viewer, navigate to the top toolbar and click on the editing icon represented by a pen, which is located adjacent to the current genome name display.
