The median sequence coverage was 6.5 (range 1.8 11.2) and the median physical coverage was 14.7 (range 6.9 28.4) (Additional files 1 and 2).
From a qualitative point of view, differences in kernel density distributions among all six datasets were especially pronounced for the West Alas population for which median sequence coverage was lower compared to the South Kinabatangan population.
Applying these stringent filters, we retained 10,930,563 bphiqual with 41× median sequence coverage for West Alas individuals and 18,186,855 bphiqual with 42× median coverage for South Kinabatangan individuals (Additional file 3: Table S2).
Duplicates were called using GATK (McKenna et al. 2010), and median sequence coverage of 10-kb nonoverlapping window was calculated from the output of samtools (Li et al. 2009) and with a combination of custom perl and R scripts.
Compared to similar studies (e.g. [ 30, 33, 42, 57]), median sequence coverage at SNP sites across all individuals in our datasets was extremely high (82× for GATK, 48× for CLC, and 27× for SAMtools), although coverage counts differed drastically among datasets.
Furthermore, our median sequence coverage of 41× (minimal cut-off of 10 reads) is substantially higher than that found in other studies, in which sequencing depth is usually between 6-16× with lower cut-off values than used in this study [ 30, 32, 33, 42, 57].
For the ultra-deep sequenced Candida albicans SC5314 transcriptome, where the median sequencing coverage of annotated protein coding genes is 175X, 4988 out of 6205 genes (80.4%) have contigs covering at least 80% of their length, demonstrating that Rnnotator is able to produce transcript sequence for the majority of the known yeast genes (Table 2).
The median sequencing coverage across the HSPG2 gene was 172X, with a range of 45X to 349X.
This analysis included 60 CpGs in the HES5 promoter and gave a median sequencing coverage of 786× (Supplementary Figure 3).
This analysis gave a median sequencing coverage of 786× (Supplementary Figure 3, see section on supplementary data given at the end of this article).
Paired-end reads of 150 bp in length were generated and a median sequencing coverage of 50X, 79X, and 107X was achieved for Dia.
