Skip navigation and go to main content

Mouse Genome Assembly GRCm39

Information on tiling path files (TPFs) for the assembly is available at TPF Overview.

Other assembly versions:
Chromosome lengths are calculated by summing the length of the placed scaffolds and estimated gaps.
Chromosome Total length (bp) GenBank accession RefSeq accession
1 195,154,279 CM000994.3 NC_000067.7
2 181,755,017 CM000995.3 NC_000068.8
3 159,745,316 CM000996.3 NC_000069.7
4 156,860,686 CM000997.3 NC_000070.7
5 151,758,149 CM000998.3 NC_000071.7
6 149,588,044 CM000999.3 NC_000072.7
7 144,995,196 CM001000.3 NC_000073.7
8 130,127,694 CM001001.3 NC_000074.7
9 124,359,700 CM001002.3 NC_000075.7
10 130,530,862 CM001003.3 NC_000076.7
11 121,973,369 CM001004.3 NC_000077.7
12 120,092,757 CM001005.3 NC_000078.7
13 120,883,175 CM001006.3 NC_000079.7
14 125,139,656 CM001007.3 NC_000080.7
15 104,073,951 CM001008.3 NC_000081.7
16 98,008,968 CM001009.3 NC_000082.7
17 95,294,699 CM001010.3 NC_000083.7
18 90,720,763 CM001011.3 NC_000084.7
19 61,420,004 CM001012.3 NC_000085.7
X 169,476,592 CM001013.3 NC_000086.8
Y 91,455,967 CM001014.3 NC_000087.8
Total lengths are calculated by summing the length of the sequenced bases and estimated gaps.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 195,974,786 195,154,279 820,507
2 181,755,017 181,755,017 0
3 159,745,316 159,745,316 0
4 156,862,662 156,860,686 1,976
5 153,496,487 151,758,149 1,738,338
6 149,588,044 149,588,044 0
7 145,171,164 144,995,196 175,968
8 130,127,694 130,127,694 0
9 124,359,700 124,359,700 0
10 130,530,862 130,530,862 0
11 121,973,369 121,973,369 0
12 120,092,757 120,092,757 0
13 120,883,175 120,883,175 0
14 125,139,656 125,139,656 0
15 104,073,951 104,073,951 0
16 98,008,968 98,008,968 0
17 95,294,699 95,294,699 0
18 90,720,763 90,720,763 0
19 61,420,004 61,420,004 0
X 170,035,695 169,476,592 559,103
Y 92,212,126 91,455,967 756,159
Un 739,257 na 739,257
Genome 2,728,206,152 2,723,414,844 4,791,308
Region Location Sequence types Scaffold length
N50 is a measure of contiguity. 50% of the bases reside in a scaffold of this length or greater.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 109,679,455 109,679,455 206,961
2 172,291,094 172,291,094 0
3 156,645,316 156,645,316 0
4 86,185,036 86,185,036 1,976
5 148,608,149 148,608,149 953,012
6 101,774,071 101,774,071 0
7 106,145,001 106,145,001 175,968
8 108,725,500 108,725,500 0
9 120,961,466 120,961,466 0
10 127,380,862 127,380,862 0
11 118,823,369 118,823,369 0
12 116,942,757 116,942,757 0
13 117,733,175 117,733,175 0
14 105,519,884 105,519,884 0
15 100,923,951 100,923,951 0
16 94,858,968 94,858,968 0
17 81,319,825 81,319,825 0
18 87,620,763 87,620,763 0
19 54,530,079 54,530,079 0
X 44,068,269 44,068,269 559,103
Y 17,801,351 17,801,351 182,347
Un 31,704 na 31,704
Genome 106,145,001 106,145,001 205,776
Region Location Sequence types Scaffold length
Ungapped lengths are calculated by summing the length of sequenced bases only. 'Ns' are excluded.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 192,774,546 191,954,039 820,507
2 178,354,017 178,354,017 0
3 156,538,186 156,538,186 0
4 152,711,764 152,709,788 1,976
5 149,744,487 148,006,149 1,738,338
6 146,383,044 146,383,044 0
7 141,850,664 141,674,696 175,968
8 125,677,394 125,677,394 0
9 121,184,854 121,184,854 0
10 127,155,762 127,155,762 0
11 118,822,369 118,822,369 0
12 116,922,757 116,922,757 0
13 117,256,175 117,256,175 0
14 121,174,156 121,174,156 0
15 100,923,951 100,923,951 0
16 94,850,968 94,850,968 0
17 91,815,499 91,815,499 0
18 87,605,763 87,605,763 0
19 58,220,004 58,220,004 0
X 164,715,435 164,206,332 509,103
Y 89,242,126 88,485,967 756,159
Un 681,617 na 681,617
Genome 2,654,605,538 2,649,921,870 4,683,668
Region Location Sequence types Scaffold length
Spanned gaps are found within scaffolds and there is some evidence suggesting linkage between the two sequences flanking the gap. Unspanned gaps are found between scaffolds and there is no evidence of linkage.
Spanned gaps Unspanned gaps
Chromosome   All scaffolds Placed scaffolds Unplaced scaffolds All scaffolds Placed scaffolds Unplaced scaffolds
1 6 6 0 6 6 0
2 2 2 0 9 9 0
3 4 4 0 4 4 0
4 29 29 0 6 6 0
5 3 3 0 5 5 0
6 1 1 0 6 6 0
7 4 4 0 6 6 0
8 6 6 0 6 6 0
9 7 7 0 5 5 0
10 2 2 0 5 5 0
11 1 1 0 5 5 0
12 1 1 0 5 5 0
13 3 3 0 5 5 0
14 3 3 0 6 6 0
15 0 0 0 5 5 0
16 3 3 0 5 5 0
17 5 5 0 6 6 0
18 1 1 0 4 4 0
19 0 0 0 6 6 0
X 50 49 1 19 19 0
Y 8 8 0 19 19 0
Un 65 na 65 0 na 0
Genome 204 138 66 143 143 0
Region Location Sequence types Scaffolds Spanned gaps Unspanned gaps
Scaffold counts.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 8 2 6
2 5 5 0
3 1 1 0
4 3 2 1
5 6 1 5
6 2 2 0
7 3 2 1
8 2 2 0
9 2 2 0
10 1 1 0
11 1 1 0
12 1 1 0
13 1 1 0
14 2 2 0
15 1 1 0
16 1 1 0
17 2 2 0
18 1 1 0
19 2 2 0
X 15 14 1
Y 20 16 4
Un 21 na 21
Genome 101 62 39
Region Location Sequence types Scaffold length
General
Assembly nameGRCm39
Release date2020-06-24
Assembly typehaploid
Release typemajor
Assembly units2
Total bases2,728,222,451
Total non-N bases2,654,621,837
Primary assembly N50106,145,001
Regions
Total regions3
Regions with alternate loci0
Regions with FIX patches0
Regions with NOVEL patches0
Regions as PAR2
Alternate loci and patches
Alternate loci0
Alternate loci aligned to primary assembly0
FIX patches0
FIX patches aligned to primary assembly0
NOVEL patches0
NOVEL patches aligned to primary assembly0