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Table 1 Properties of the sequence data

From: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

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%)
  1. aValues in parentheses are those without reads entirely composed of uncalled bases. At, Arabidopsis thaliana; Bv, Beta vulgaris; PhiX, bacteriophage PhiX174.