BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238501.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 = 4,915,929 number of mapped reads = 4,250,671 (86.47%) number of supplementary alignments = 32,907 (0.67%) number of secondary alignments = 0 number of mapped bases = 259,070,465 bp number of sequenced bases = 258,890,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,089,025 duplication rate = 18.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2636 >>>>>>> ACTG content number of A's = 64,227,022 bp (24.81%) number of C's = 45,317,264 bp (17.5%) number of T's = 87,245,680 bp (33.7%) number of G's = 62,083,141 bp (23.98%) number of N's = 17,078 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,743,368 number of insertions = 17,533 mapped reads with insertion percentage = 0.41% number of deletions = 106,396 mapped reads with deletion percentage = 2.47% homopolymer indels = 40.78% >>>>>>> Coverage mean coverageData = 0.0837X std coverageData = 1.1578X There is a 4.26% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 27106351 0.10875138802562903 1.4301251189616724 chr2 243199373 10135717 0.04167657537505247 2.9241463920035073 chr3 198022430 34067919 0.1720407077117476 0.7555323034846528 chr4 191154276 10659679 0.05576479492407484 0.43174747106569134 chr5 180915260 15388149 0.0850572196065716 0.5262914761046157 chr6 171115067 18278882 0.10682216546132668 1.0340879335553113 chr7 159138663 10571858 0.0664317382131079 0.9226781876227182 chr8 146364022 22713163 0.155182692369577 1.0008378501101962 chr9 141213431 8418750 0.0596172045419674 0.5601955987982902 chr10 135534747 15368696 0.11339303271064505 0.8552381414448814 chr11 135006516 8019913 0.059403895734928824 0.4829709818379844 chr12 133851895 2643222 0.019747363307781336 0.2853679730105612 chr13 115169878 6777612 0.058848825037393894 0.7194432253376198 chr14 107349540 6704020 0.06245038404449614 0.4680485840176273 chr15 102531392 6197084 0.06044084527790279 0.6730143892183577 chr16 90354753 4842409 0.053593295750584365 0.5728532064482755 chr17 81195210 4540437 0.05592001055234662 0.4283078482559281 chr18 78077248 12780547 0.16369105376255064 2.147873613726417 chr19 59128983 3325629 0.05624363605239075 0.9436749232503009 chr20 63025520 1938219 0.030752923577623794 0.3461409014276733 chr21 48129895 5278599 0.10967401861150954 0.6111834597056984 chr22 51304566 972151 0.01894862535237117 0.228368105577083 chrMT 16571 47335 2.8564962886971217 3.321641493502641 chrX 155270560 21466909 0.1382548565549065 0.7086853950802063 chrY 59373566 827215 0.0139323785942047 0.4390921168788807