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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 nameGRCz11
Release date2017-05-09
Assembly typehaploid-with-alt-loci
Release typemajor
Assembly units5
Total bases1,679,186,873
Total non-N bases1,674,495,211
Primary assembly N507,379,053
Regions
Total regions607
Regions with alternate loci607
Regions with FIX patches0
Regions with NOVEL patches0
Regions as PAR0
Alternate loci and patches
Alternate loci930
Alternate loci aligned to primary assembly930
FIX patches0
FIX patches aligned to primary assembly0
NOVEL patches0
NOVEL patches aligned to primary assembly0