Zebrafish Genome Assembly GRCz11

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	59,578,282	CM002885.2	NC_007112.7
2	59,640,629	CM002886.2	NC_007113.7
3	62,628,489	CM002887.2	NC_007114.7
4	78,093,715	CM002888.2	NC_007115.7
5	72,500,376	CM002889.2	NC_007116.7
6	60,270,059	CM002890.2	NC_007117.7
7	74,282,399	CM002891.2	NC_007118.7
8	54,304,671	CM002892.2	NC_007119.7
9	56,459,846	CM002893.2	NC_007120.7
10	45,420,867	CM002894.2	NC_007121.7
11	45,484,837	CM002895.2	NC_007122.7
12	49,182,954	CM002896.2	NC_007123.7
13	52,186,027	CM002897.2	NC_007124.7
14	52,660,232	CM002898.2	NC_007125.7
15	48,040,578	CM002899.2	NC_007126.7
16	55,266,484	CM002900.2	NC_007127.7
17	53,461,100	CM002901.2	NC_007128.7
18	51,023,478	CM002902.2	NC_007129.7
19	48,449,771	CM002903.2	NC_007130.7
20	55,201,332	CM002904.2	NC_007131.7
21	45,934,066	CM002905.2	NC_007132.7
22	39,133,080	CM002906.2	NC_007133.7
23	46,223,584	CM002907.2	NC_007134.7
24	42,172,926	CM002908.2	NC_007135.7
25	37,502,051	CM002909.2	NC_007136.7

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

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	59,578,282	59,578,282	0
2	59,640,629	59,640,629	0
3	62,628,489	62,628,489	0
4	78,093,715	78,093,715	0
5	72,500,376	72,500,376	0
6	60,270,059	60,270,059	0
7	74,282,399	74,282,399	0
8	54,304,671	54,304,671	0
9	56,459,846	56,459,846	0
10	45,420,867	45,420,867	0
11	45,484,837	45,484,837	0
12	49,182,954	49,182,954	0
13	52,186,027	52,186,027	0
14	52,660,232	52,660,232	0
15	48,040,578	48,040,578	0
16	55,266,484	55,266,484	0
17	53,461,100	53,461,100	0
18	51,023,478	51,023,478	0
19	48,449,771	48,449,771	0
20	55,201,332	55,201,332	0
21	45,934,066	45,934,066	0
22	39,133,080	39,133,080	0
23	46,223,584	46,223,584	0
24	42,172,926	42,172,926	0
25	37,502,051	37,502,051	0
Un	28,352,955	na	28,352,955
Genome	1,373,454,788	1,345,101,833	28,352,955

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	4,818,344	4,818,344	0
2	5,197,540	5,197,540	0
3	4,572,487	4,572,487	0
4	7,379,053	7,379,053	0
5	13,500,411	13,500,411	0
6	9,977,335	9,977,335	0
7	5,009,329	5,009,329	0
8	8,083,138	8,083,138	0
9	32,000,149	32,000,149	0
10	4,706,895	4,706,895	0
11	7,242,237	7,242,237	0
12	32,399,083	32,399,083	0
13	8,482,599	8,482,599	0
14	28,653,342	28,653,342	0
15	29,777,154	29,777,154	0
16	14,334,442	14,334,442	0
17	5,946,312	5,946,312	0
18	15,551,655	15,551,655	0
19	11,329,993	11,329,993	0
20	9,260,504	9,260,504	0
21	4,066,630	4,066,630	0
22	5,145,648	5,145,648	0
23	3,380,090	3,380,090	0
24	4,737,936	4,737,936	0
25	4,876,667	4,876,667	0
Un	48,672	na	48,672
Genome	7,379,053	7,538,642	48,672

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

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	59,518,204	59,518,204	0
2	59,561,129	59,561,129	0
3	62,565,097	62,565,097	0
4	75,268,643	75,268,643	0
5	72,411,310	72,411,310	0
6	60,194,477	60,194,477	0
7	74,193,585	74,193,585	0
8	54,255,784	54,255,784	0
9	56,393,308	56,393,308	0
10	45,373,267	45,373,267	0
11	45,418,283	45,418,283	0
12	49,092,027	49,092,027	0
13	52,124,602	52,124,602	0
14	52,604,632	52,604,632	0
15	47,971,581	47,971,581	0
16	55,207,672	55,207,672	0
17	53,387,590	53,387,590	0
18	50,931,061	50,931,061	0
19	48,391,784	48,391,784	0
20	55,132,661	55,132,661	0
21	45,869,123	45,869,123	0
22	39,045,925	39,045,925	0
23	46,157,041	46,157,041	0
24	42,107,172	42,107,172	0
25	37,439,205	37,439,205	0
Un	28,150,343	na	28,150,343
Genome	1,368,765,506	1,340,615,163	28,150,343

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	561	561	0	35	35	0
2	741	741	0	54	54	0
3	594	594	0	38	38	0
4	440	440	0	48	48	0
5	824	824	0	71	71	0
6	722	722	0	35	35	0
7	835	835	0	54	54	0
8	460	460	0	27	27	0
9	642	642	0	25	25	0
10	446	446	0	30	30	0
11	626	626	0	40	40	0
12	881	881	0	29	29	0
13	582	582	0	33	33	0
14	528	528	0	28	28	0
15	663	663	0	28	28	0
16	559	559	0	29	29	0
17	695	695	0	41	41	0
18	897	897	0	22	22	0
19	545	545	0	35	35	0
20	645	645	0	43	43	0
21	603	603	0	48	48	0
22	454	454	0	23	23	0
23	635	635	0	30	30	0
24	622	622	0	35	35	0
25	584	584	0	44	44	0
Un	2,027	na	2,027	0	na	0
Genome	17,811	15,784	2,027	925	925	0

Scaffold counts.

Chromosome	All scaffolds	Placed scaffolds	Unplaced scaffolds
1	36	36	0
2	55	55	0
3	39	39	0
4	49	49	0
5	72	72	0
6	36	36	0
7	55	55	0
8	28	28	0
9	26	26	0
10	31	31	0
11	41	41	0
12	30	30	0
13	34	34	0
14	29	29	0
15	29	29	0
16	30	30	0
17	42	42	0
18	23	23	0
19	36	36	0
20	44	44	0
21	49	49	0
22	24	24	0
23	31	31	0
24	36	36	0
25	45	45	0
Un	967	na	967
Genome	1,917	950	967

General
Assembly name	GRCz11
Release date	2017-05-09
Assembly type	haploid-with-alt-loci
Release type	major
Assembly units	5
Total bases	1,679,186,873
Total non-N bases	1,674,495,211
Primary assembly N50	7,379,053

Regions
Total regions	607
Regions with alternate loci	607
Regions with FIX patches	0
Regions with NOVEL patches	0
Regions as PAR	0

Alternate loci and patches
Alternate loci	930
Alternate loci aligned to primary assembly	930
FIX patches	0
FIX patches aligned to primary assembly	0
NOVEL patches	0
NOVEL patches aligned to primary assembly	0