Table 3 Summary of human contig assembly
From: BASE: a practical de novo assembler for large genomes using long NGS reads
YH, 100 bp | YH, 150 bp | NA12878, 150 bp | NA12878, 250 bp | |||||
|---|---|---|---|---|---|---|---|---|
SOAPdenovo2,k = 41 | BASE | SOAPdenovo2,k = 61 | BASE | SOAPdenovo2,k = 41 | BASE | SOAPdenovo2,k = 61 | BASE | |
Contig num | 3,420,897 | 3,319,617 | 2,279,026 | 2,145,792 | 8,068,278 | 1,934,261 | 1,416,658 | 1,511,270 |
Contig size | 2.67E + 09 | 2.88E + 09 | 2.76E + 09 | 2.95E + 09 | 2.44E + 09 | 2.90E + 09 | 2.60E + 09 | 2.94E + 09 |
Contig N50 | 2,244 | 2,279 | 3,008 | 3,126 | 1,140 | 3,823 | 3,368 | 4,199 |
Contig aligned rate | 99.10 % | 97.07 % | 98.87 % | 95.96 % | 99.40 % | 97.62 % | 99.34 % | 96.33 % |
Genome coverage | 90.36 % | 93.76 % | 93.12 % | 93.90 % | 84.11 % | 95.58 % | 89.55 % | 94.09 % |
RepeatMasked coverage | 97.05 % | 96.13 % | 97.28 % | 95.32 % | 93.94 % | 97.38 % | 95.60 % | 95.99 % |
Exon coverage | 93.76 % | 91.51 % | 95.73 % | 94.13 % | 91.48 % | 96.84 % | 93.90 % | 91.49 % |
Mismatch base | 2,735,141 | 3,479,046 | 2,911,990 | 3,839,110 | 2,301,111 | 3,459,648 | 2,544,785 | 3,751,887 |
Mismatch ratio | 0.103 % | 0.121 % | 0.105 % | 0.130 % | 0.094 % | 0.119 % | 0.098 % | 0.128 % |
Indel num | 340,930 | 327,469 | 358,358 | 334,989 | 259,190 | 322,214 | 327,695 | 372,941 |
Indel base | 1,412,005 | 1,587,265 | 1,692,213 | 1,741,947 | 1,086,014 | 1,602,240 | 1,400,230 | 1,953,311 |
Indel ratio | 0.053 % | 0.057 % | 0.062 % | 0.061 % | 0.045 % | 0.057 % | 0.054 % | 0.069 % |