Alignment files are sorted by Picard. Then I use Samtools mpileup function to create a pileup file of mapped data prepared for DNA methylation–level calculation. The output seems good. But I find it miss some base at start. What about the first five bases ? Why does it start from the sixth base of chrM ?

This is my command : samtools mpileup -f <genome.fa> <read1_val_1.sort.bam> > <read1_val_1.pileup>

Thank you very much !

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chrM 6 C 0

chrM 7 A 0

chrM 8 G 0

chrM 9 G 0

chrM 10 T 4 .... U=RR

chrM 11 C 4 .... _:fc

chrM 12 T 4 .... dBfg

chrM 13 A 7 T...^K.^!.^). dBec033

chrM 14 T 11 .......^K.^K.^K.^K. cFgh0U3C@C@

chrM 15 C 11 ....TT...., XFVc03C<c@:< p="">

chrM 16 A 11 .....C....,-1c `F\03OY]W8

chrM 17 C 11 ....TAA.... iFek033igii

......

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