Table 1.
Properties of the sequence data
| Species | Bv + PhiX | At + PhiX | PhiX |
|---|---|---|---|
| Platform | HiSeq | HiSeq | GAIIx |
| Read length | 95 | 100 | 150 |
| Number of lanes | 3 | 1 | 1 |
| Number of sequenced pairs | 246,159,940 | 71,393,237 | 9,046,254 |
| Number of sequenced bases | 46,770,388,600 | 14,278,647,400 | 2,713,876,200 |
| Fraction of uncalled bases | 1.52% | 1.21% | 13.77% |
| Fraction of uncalled bases - read 1 | 1.45% | 1.07% | 12.66% |
| Fraction of uncalled bases - read 2 | 1.58% | 1.34% | 14.87% |
| Fraction of reads with at least one uncalled base | 2.46% | 2.26% | 15.57% |
| Fraction of entirely uncalled reads | 0.56% | 0.50% | 7.16% |
| Fraction of bases in B-tails | 11.01% | 16.56% | 25.78% |
| Fraction of uncalled bases in B-tails | 1.49% | 1.18% | 13.75% |
| Fraction of bases in B-tails - read 1 | 11.02% | 14.45% | 24.82% |
| Fraction of bases in B-tails - read 2 | 11.00% | 18.67% | 26.74% |
| Average length of B-tails | 10.5 (9.9)a | 16.6 (16.1)a | 38.7 (27.9)a |
| Fraction of reads with B-tail | 26.15% | 39.44% | 67.87% |
| Fraction of reads containing at least one uncalled base in B-tail | 2.19% | 1.98% | 14.99% |
| Fraction of both reads with B-tail | 14.70% | 24.50% | 53.10% |
| Average Q-score | 31.81 | 30.23 | 27.17 |
| Average Q-score - read 1 | 31.83 | 31.10 | 27.62 |
| Average Q-score - read 2 | 31.80 | 29.37 | 26.73 |
| Q ≥ 30 bases | 37.27 Gbp (79.68%) | 10.56 Gbp (73.99%) | 1.74 Gbp (64.29%) |
| Q ≥ 30 bases - read 1 | 18.70 Gbp (39.98%) | 5.49 Gbp (38.42%) | 0.90 Gbp (33.01%) |
| Q ≥ 30 bases - read 2 | 18.57 Gbp (39.71%) | 5.08 Gbp (35.57%) | 0.85 Gbp (31.28%) |
aValues in parentheses are those without reads entirely composed of uncalled bases. At, Arabidopsis thaliana; Bv, Beta vulgaris; PhiX, bacteriophage PhiX174.