BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716679.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,927,964 number of mapped reads = 1,750,952 (90.82%) number of supplementary alignments = 9,663 (0.5%) number of secondary alignments = 0 number of mapped bases = 102,171,843 bp number of sequenced bases = 102,142,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,824 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5315 >>>>>>> ACTG content number of A's = 24,561,995 bp (24.05%) number of C's = 19,571,722 bp (19.16%) number of T's = 32,221,198 bp (31.55%) number of G's = 25,786,604 bp (25.25%) number of N's = 702 bp (0%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 517,574 number of insertions = 6,585 mapped reads with insertion percentage = 0.37% number of deletions = 18,485 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2956X There is a 2.89% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 12709359 0.05099028018068609 0.47474109805111275 chr2 243199373 10562940 0.04343325342372491 0.43183895966079494 chr3 198022430 6426291 0.03245233885878484 0.20067958836383953 chr4 191154276 4319135 0.022595021625359823 0.19392013335317287 chr5 180915260 7261853 0.0401395272018513 0.22363286177538755 chr6 171115067 3753664 0.021936490256582723 0.188614261190415 chr7 159138663 6892468 0.04331108399471724 0.4784506861933374 chr8 146364022 4611943 0.03151008654298937 0.25742895194909915 chr9 141213431 2831064 0.02004812134335862 0.2190982262557643 chr10 135534747 4655734 0.03435085174136194 0.25760934913407757 chr11 135006516 4333022 0.0320949101449296 0.2793042368292445 chr12 133851895 4144901 0.03096632288993742 0.19829661401014353 chr13 115169878 3039396 0.02639054631975906 0.18085565209580964 chr14 107349540 1387048 0.01292085648434078 0.13909001193906104 chr15 102531392 4425848 0.04316578477740749 0.23353046293286014 chr16 90354753 3037471 0.03361716898279828 0.21451210423718162 chr17 81195210 3879155 0.04777566312101416 0.2664372419773173 chr18 78077248 3241393 0.04151520555642535 0.4805888622623666 chr19 59128983 1636546 0.027677560427514878 0.3617810956484845 chr20 63025520 2682636 0.042564281897237814 0.23186419270158262 chr21 48129895 965493 0.020060151803780166 0.17439017723945177 chr22 51304566 1327888 0.025882452645637818 0.17998225400758966 chrMT 16571 8881 0.5359362742139883 0.8556941752177378 chrX 155270560 3791902 0.024421255388014314 0.2017126762798992 chrY 59373566 245812 0.004140091568695739 0.1087041660251669