Resource
| Id | reference/Mouse/genome/GRCm39 |
|---|---|
| Type | genome |
| Version | 0 |
| Summary |
Mouse (Mus musculus) GRCm39 reference genome
|
| Description |
GENCODE genome assembly GRCm39 for the house mouse (Mus musculus), in FASTA format. Downloaded from: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M39/GRCm39.genome.fa.gz Download date: 8/31/2026 Downloaded gzip was recompressed with bgzip and indexed with samtools faidx. |
| Labels |
Chromosomes (61):
| Chrom | Length | A | T | C | G | N |
|---|---|---|---|---|---|---|
| Global | 2,728,222,451 | 28.36% | 28.40% | 20.27% | 20.27% | 2.70% |
| chr1 | 195,154,279 | 28.97% | 28.92% | 20.24% | 20.23% | 1.64% |
| chr2 | 181,755,017 | 28.39% | 28.44% | 20.64% | 20.66% | 1.87% |
| chr3 | 159,745,316 | 29.14% | 29.22% | 19.80% | 19.84% | 2.01% |
| chr4 | 156,860,686 | 28.06% | 28.13% | 20.57% | 20.59% | 2.65% |
| chr5 | 151,758,149 | 28.01% | 28.03% | 20.74% | 20.74% | 2.47% |
| chr6 | 149,588,044 | 28.65% | 28.68% | 20.27% | 20.26% | 2.14% |
| chr7 | 144,995,196 | 27.73% | 27.90% | 21.05% | 21.03% | 2.29% |
| chr8 | 130,127,694 | 27.85% | 27.81% | 20.47% | 20.45% | 3.42% |
| chr9 | 124,359,700 | 27.93% | 27.91% | 20.82% | 20.80% | 2.55% |
| chr10 | 130,530,862 | 28.51% | 28.58% | 20.15% | 20.19% | 2.59% |
| chr11 | 121,973,369 | 27.41% | 27.33% | 21.34% | 21.34% | 2.58% |
| chr12 | 120,092,757 | 28.23% | 28.50% | 20.30% | 20.34% | 2.64% |
| chr13 | 120,883,175 | 28.37% | 28.26% | 20.19% | 20.18% | 3.00% |
| chr14 | 125,139,656 | 28.45% | 28.53% | 19.92% | 19.93% | 3.17% |
| chr15 | 104,073,951 | 28.11% | 28.17% | 20.35% | 20.34% | 3.03% |
| chr16 | 98,008,968 | 28.55% | 28.60% | 19.80% | 19.82% | 3.22% |
| chr17 | 95,294,699 | 27.58% | 27.63% | 20.58% | 20.56% | 3.65% |
| chr18 | 90,720,763 | 28.28% | 28.27% | 19.98% | 20.03% | 3.43% |
| chr19 | 61,420,004 | 27.25% | 27.04% | 20.27% | 20.23% | 5.21% |
| chrX | 169,476,592 | 29.43% | 29.42% | 19.01% | 19.03% | 3.11% |
| chrY | 91,455,967 | 29.48% | 29.66% | 18.86% | 18.77% | 3.25% |
| chrM | 16,299 | 34.54% | 28.72% | 24.39% | 12.35% | 0.00% |
| GL456210.1 | 169,725 | 27.47% | 28.52% | 22.11% | 21.90% | 0.00% |
| GL456211.1 | 241,735 | 28.27% | 27.81% | 22.25% | 21.67% | 0.00% |
| GL456212.1 | 153,618 | 27.67% | 28.60% | 22.04% | 21.69% | 0.00% |
| GL456219.1 | 175,968 | 28.64% | 31.23% | 19.82% | 20.30% | 0.00% |
| GL456221.1 | 206,961 | 28.49% | 27.96% | 21.38% | 22.18% | 0.00% |
| GL456233.2 | 559,103 | 27.33% | 29.28% | 17.29% | 17.16% | 8.94% |
| GL456239.1 | 40,056 | 30.18% | 27.31% | 21.00% | 21.51% | 0.00% |
| GL456354.1 | 195,993 | 31.84% | 27.04% | 20.58% | 20.54% | 0.00% |
| GL456359.1 | 22,974 | 30.15% | 30.87% | 18.62% | 19.93% | 0.44% |
| GL456360.1 | 31,704 | 30.22% | 28.79% | 20.19% | 19.66% | 1.14% |
| GL456366.1 | 47,073 | 28.01% | 24.48% | 17.87% | 18.22% | 11.42% |
| GL456367.1 | 42,057 | 29.33% | 31.12% | 17.12% | 19.02% | 3.40% |
| GL456368.1 | 20,208 | 33.20% | 28.22% | 18.58% | 18.42% | 1.58% |
| GL456370.1 | 26,764 | 26.80% | 28.40% | 12.28% | 9.99% | 22.52% |
| GL456372.1 | 28,664 | 21.92% | 22.98% | 19.07% | 17.72% | 18.31% |
| GL456378.1 | 31,602 | 27.08% | 30.12% | 19.32% | 19.75% | 3.73% |
| GL456379.1 | 72,385 | 29.60% | 30.26% | 18.21% | 18.75% | 3.18% |
| GL456381.1 | 25,871 | 25.82% | 16.27% | 16.89% | 21.25% | 19.78% |
| GL456382.1 | 23,158 | 31.04% | 28.92% | 18.18% | 18.50% | 3.36% |
| GL456383.1 | 38,659 | 15.40% | 35.75% | 17.99% | 11.58% | 19.29% |
| GL456385.1 | 35,240 | 29.01% | 31.68% | 19.45% | 19.58% | 0.28% |
| GL456387.1 | 24,685 | 28.45% | 16.02% | 19.41% | 23.75% | 12.37% |
| GL456389.1 | 28,772 | 16.16% | 34.87% | 18.53% | 18.57% | 11.86% |
| GL456390.1 | 24,668 | 24.01% | 9.43% | 7.82% | 12.04% | 46.70% |
| GL456392.1 | 23,629 | 37.67% | 23.92% | 15.60% | 20.86% | 1.96% |
| GL456394.1 | 24,323 | 28.82% | 24.03% | 17.09% | 19.12% | 10.93% |
| GL456396.1 | 21,240 | 34.81% | 21.62% | 18.15% | 21.95% | 3.46% |
| JH584295.1 | 1,976 | 19.18% | 18.98% | 30.92% | 30.92% | 0.00% |
| JH584296.1 | 199,368 | 31.36% | 27.65% | 20.58% | 20.42% | 0.00% |
| JH584297.1 | 205,776 | 30.70% | 28.37% | 20.44% | 20.49% | 0.00% |
| JH584298.1 | 184,189 | 27.98% | 30.97% | 20.39% | 20.66% | 0.00% |
| JH584299.1 | 953,012 | 28.29% | 30.67% | 20.64% | 20.41% | 0.00% |
| JH584300.1 | 182,347 | 30.42% | 30.21% | 19.46% | 19.91% | 0.00% |
| JH584301.1 | 259,875 | 31.29% | 29.52% | 19.10% | 20.09% | 0.00% |
| JH584302.1 | 155,838 | 32.16% | 28.84% | 19.27% | 19.73% | 0.00% |
| JH584303.1 | 158,099 | 30.99% | 29.19% | 20.07% | 19.76% | 0.00% |
| JH584304.1 | 114,452 | 22.81% | 35.02% | 22.72% | 19.45% | 0.00% |
| MU069434.1 | 8,412 | 28.32% | 23.53% | 24.86% | 23.30% | 0.00% |
| MU069435.1 | 31,129 | 23.98% | 34.31% | 21.55% | 20.16% | 0.00% |
Bi-Nucleotide distribution:
| A | T | C | G | N | |
|---|---|---|---|---|---|
| A | 8.87% | 7.18% | 5.18% | 7.14% | 0.00% |
| T | 6.20% | 8.89% | 6.06% | 7.25% | 0.00% |
| C | 7.24% | 7.14% | 5.08% | 0.80% | 0.00% |
| G | 6.05% | 5.19% | 3.95% | 5.08% | 0.00% |
| N | 0.00% | 0.00% | 0.00% | 0.00% | 2.70% |
Files
| Filename | Size | md5 |
|---|---|---|
| GRCm39.genome.fa.gz | 696.16 MB | 582525dd58edd446396e45f404a1d76d |
| GRCm39.genome.fa.gz.fai | 1.98 KB | 4a9d6c298e54550773d9c993576d6ce8 |
| GRCm39.genome.fa.gz.gzi | 663.99 KB | 0ba0c3a473c11e30d10d927ea0d57c74 |
| genomic_resource.yaml | 444.0 B | 6a587cfbba8fb3b7276128cbd8baef46 |
| statistics/ |