BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238514.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,619,470 number of mapped reads = 2,351,505 (89.77%) number of supplementary alignments = 19,017 (0.73%) number of secondary alignments = 0 number of mapped bases = 143,587,608 bp number of sequenced bases = 143,525,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 828,219 duplication rate = 22.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5427 >>>>>>> ACTG content number of A's = 34,236,315 bp (23.85%) number of C's = 25,184,071 bp (17.55%) number of T's = 48,549,902 bp (33.83%) number of G's = 35,545,887 bp (24.77%) number of N's = 9,251 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 786,339 number of insertions = 9,107 mapped reads with insertion percentage = 0.39% number of deletions = 36,827 mapped reads with deletion percentage = 1.55% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 0.0464X std coverageData = 0.8148X There is a 1.79% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16854141 0.06761925379515905 0.6978954069743296 chr2 243199373 17298528 0.07112899916892466 2.0866308988147706 chr3 198022430 11666901 0.05891706813213028 0.5468706270404794 chr4 191154276 4661715 0.024387186609416994 0.3322884236863033 chr5 180915260 3463184 0.01914257536926404 0.30318056545943134 chr6 171115067 9173720 0.053611409917514743 0.806358158969981 chr7 159138663 9332925 0.05864649623203131 0.9454289884920017 chr8 146364022 6734208 0.04600999554385025 0.5347813479111362 chr9 141213431 3830132 0.027123000785952152 0.3905324206738703 chr10 135534747 7213674 0.05322379802723209 0.5366944378866729 chr11 135006516 2246204 0.016637745099651338 0.274171910585032 chr12 133851895 8231657 0.06149824774613762 0.564966390223312 chr13 115169878 892458 0.00774905744017546 0.3981952381206033 chr14 107349540 4757489 0.04431773997354809 0.476853822118638 chr15 102531392 3670939 0.035803073852737705 0.5484189878637423 chr16 90354753 1930270 0.02136323697326692 0.34829885751855894 chr17 81195210 4745266 0.05844268399576773 0.5454381597773695 chr18 78077248 6058426 0.07759528102219997 1.355841316929697 chr19 59128983 4424081 0.07482085392877466 0.6772220651018255 chr20 63025520 2571097 0.04079453846632285 0.44763160999245943 chr21 48129895 2635533 0.05475875233054217 0.5373610819654802 chr22 51304566 1650631 0.032173179283886744 0.397866283507477 chrMT 16571 191642 11.564902540582946 10.970489420110127 chrX 155270560 8982933 0.0578534205067593 0.5362390413274066 chrY 59373566 369854 0.006229270446716979 0.2947907654164512