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Table 1 Data statistics of the crested ibis and the little egret

From: Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

  Crested ibis Little egret
De novo sequence
Insert size (bp) Total data (Gb) Sequence coverage ( x genome) Total data (Gb) Sequence coverage (x genome)
170-800 141 113 53 42
2-20 × 103 54 43 36 29
Total 195 156 89 71
Assembly
  N50 (kb) Total size (Gb) N50 (kb) Total size (Gb)
Contigs 67 1.24 24 1.16
Scaffolds 10,687 1.26 3,051 1.21
Annotation
  Number Total length (Mb) Number Total length (Mb)
Repeats 840,220 80 861,413 86
Genes 17,179 343 17,032 326
Coding exons 148,003 24 139,080 23
Resequencinga
  Total data (Gb) Sequence coverage (x genome) Total data (Gb) Sequence coverage (x genome)
Each individual 25 20 30 24
All individuals 200 160 149 119
SNP calling
  Total SNPs Mutation rateb (θS) (×10-3) Total SNPs Mutation rateb (θS) (×10-3)
Autosome 1,188,930 0.33 8,876,153 2.91
Coding exons 13,459 0.17 91,820 1.45
  1. aPaired-end libraries with insert size of 500 bp were used for resequencing. Samples were from eight crested ibis and five little egrets.
  2. bThe population mutation parameter θS = K/aL, a = 1 + 1/2 + … + 1/(n-1), where K is the number of variant sites found by sequencing n chromosomes in a region of length L.
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Genome Biology

ISSN: 1474-760X

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