Rat Genome Assembly GRCr8

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	270,518,180	CM070391.1	NC_086019.1
2	251,712,708	CM070392.1	NC_086020.1
3	189,428,310	CM070393.1	NC_086021.1
4	184,426,481	CM070394.1	NC_086022.1
5	172,190,305	CM070395.1	NC_086023.1
6	147,156,653	CM070396.1	NC_086024.1
7	137,014,596	CM070397.1	NC_086025.1
8	132,782,436	CM070398.1	NC_086026.1
9	121,768,150	CM070399.1	NC_086027.1
10	107,713,808	CM070400.1	NC_086028.1
11	99,753,367	CM070401.1	NC_086029.1
12	52,308,831	CM070402.1	NC_086030.1
13	109,350,286	CM070403.1	NC_086031.1
14	109,089,856	CM070404.1	NC_086032.1
15	108,192,169	CM070405.1	NC_086033.1
16	91,442,908	CM070406.1	NC_086034.1
17	93,515,804	CM070407.1	NC_086035.1
18	86,134,022	CM070408.1	NC_086036.1
19	74,246,245	CM070409.1	NC_086037.1
20	56,021,148	CM070410.1	NC_086038.1
X	157,758,123	CM070411.1	NC_086039.1
Y	59,846,084	CM070412.1	NC_086040.1

Total lengths are calculated by summing the length of the sequenced bases and estimated gaps.

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	270,518,180	270,518,180	0
2	251,712,708	251,712,708	0
3	193,850,820	189,428,310	4,422,510
4	184,426,481	184,426,481	0
5	172,190,305	172,190,305	0
6	147,156,653	147,156,653	0
7	137,014,596	137,014,596	0
8	132,782,436	132,782,436	0
9	121,768,150	121,768,150	0
10	107,713,808	107,713,808	0
11	99,753,367	99,753,367	0
12	52,308,831	52,308,831	0
13	109,350,286	109,350,286	0
14	109,089,856	109,089,856	0
15	108,192,169	108,192,169	0
16	91,442,908	91,442,908	0
17	93,515,804	93,515,804	0
18	86,134,022	86,134,022	0
19	74,246,245	74,246,245	0
20	56,021,148	56,021,148	0
X	157,758,123	157,758,123	0
Y	92,364,546	59,846,084	32,518,462
Genome	2,849,581,192	2,812,370,470	37,210,722

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	270,518,180	270,518,180	0
2	251,712,708	251,712,708	0
3	189,428,310	189,428,310	2,449,928
4	184,426,481	184,426,481	0
5	172,190,305	172,190,305	0
6	147,156,653	147,156,653	0
7	137,014,596	137,014,596	0
8	132,782,436	132,782,436	0
9	121,768,150	121,768,150	0
10	107,713,808	107,713,808	0
11	99,753,367	99,753,367	0
12	52,308,831	52,308,831	0
13	109,350,286	109,350,286	0
14	109,089,856	109,089,856	0
15	108,192,169	108,192,169	0
16	91,442,908	91,442,908	0
17	93,515,804	93,515,804	0
18	86,134,022	86,134,022	0
19	74,246,245	74,246,245	0
20	56,021,148	56,021,148	0
X	157,758,123	157,758,123	0
Y	59,846,084	59,846,084	903,984
Genome	137,014,596	137,014,596	903,984

Ungapped lengths are calculated by summing the length of sequenced bases only. 'Ns' are excluded.

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	270,167,028	270,167,028	0
2	251,671,381	251,671,381	0
3	193,790,736	189,368,226	4,422,510
4	184,252,369	184,252,369	0
5	172,120,554	172,120,554	0
6	147,155,907	147,155,907	0
7	136,990,387	136,990,387	0
8	132,742,312	132,742,312	0
9	121,767,304	121,767,304	0
10	107,713,808	107,713,808	0
11	99,751,644	99,751,644	0
12	52,308,308	52,308,308	0
13	109,344,646	109,344,646	0
14	109,063,146	109,063,146	0
15	107,526,243	107,526,243	0
16	91,428,241	91,428,241	0
17	93,515,704	93,515,704	0
18	86,132,090	86,132,090	0
19	73,926,054	73,926,054	0
20	56,018,448	56,018,448	0
X	157,468,448	157,468,448	0
Y	90,326,107	59,836,953	30,489,154
Genome	2,845,450,615	2,810,269,201	35,181,414

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	21	21	0	0	0	0
2	6	6	0	0	0	0
3	17	17	0	0	0	0
4	13	13	0	0	0	0
5	1	1	0	0	0	0
6	4	4	0	0	0	0
7	7	7	0	0	0	0
8	8	8	0	0	0	0
9	5	5	0	0	0	0
10	0	0	0	0	0	0
11	7	7	0	0	0	0
12	4	4	0	0	0	0
13	2	2	0	0	0	0
14	2	2	0	0	0	0
15	11	11	0	0	0	0
16	4	4	0	0	0	0
17	1	1	0	0	0	0
18	2	2	0	0	0	0
19	9	9	0	0	0	0
20	1	1	0	0	0	0
X	10	10	0	0	0	0
Y	85	29	56	0	0	0
Genome	220	164	56	0	0	0

Scaffold counts.

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	1	1	0
2	1	1	0
3	6	1	5
4	1	1	0
5	1	1	0
6	1	1	0
7	1	1	0
8	1	1	0
9	1	1	0
10	1	1	0
11	1	1	0
12	1	1	0
13	1	1	0
14	1	1	0
15	1	1	0
16	1	1	0
17	1	1	0
18	1	1	0
19	1	1	0
20	1	1	0
X	1	1	0
Y	47	1	46
Genome	76	22	54

General
Assembly name	GRCr8
Release date	2024-01-31
Assembly type	haploid
Release type	major
Assembly units	2
Total bases	2,849,597,507
Total non-N bases	2,845,466,930
Primary assembly N50	137,014,596

Regions
Total regions	0
Regions with alternate loci	0
Regions with FIX patches	0
Regions with NOVEL patches	0
Regions as PAR	0

Alternate loci and patches
Alternate loci	0
Alternate loci aligned to primary assembly	0
FIX patches	0
FIX patches aligned to primary assembly	0
NOVEL patches	0
NOVEL patches aligned to primary assembly	0