Table 1 of Hoang, Mol Vis 2014; 20:1491-1517.

Table 1. Summary of base calling and alignments.

Sequence reads E1 E2 E3 F1 F2 F3
Total raw reads 33,174,286 29,919,226 29,965,660 28,652,759 30,661,663 24,833,352
Reads passed quality filtering 30,524,674
(92%) 27,392,629
(91.5%) 28,203,944
(94.1%) 27,019,907
(94.3%) 27,760,247
(90.5%) 22,735,990
(91.6%)
Mapped reads 29,414,088
(89%) 27,286,119
(91%) 27,299,912
(91.1%) 25,814,802
(90%) 27,495,080
(89.6%) 22,630,822
(91.1%)
Uniquely and perfectly mapped reads 12,925,906
(39%)* 18,954,231
(63.3%) 18,408,241
(61.4%) 18,686,534
(65.2%) 18,354,154
(59.8%) 15,975,465
(64.3%)

* Although all 6 samples have similar percentages of mapped reads, we found a higher number of reads that mapped ambiguously to reference genome in E1 samples than the other 5 samples. We used other mapping tools to verify these results with similar outcome. We do not know why the E1 sample contains fewer unique reads, and at this point any explanation for this discrepancy would be speculation on our part.

Hoang, Mol Vis 2014; 20:1491-1517. http://www.molvis.org/molvis/v20/1491

©2014 Molecular Vision http://www.molvis.org/molvis/

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