BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013220.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 = 1,753,352 number of mapped reads = 1,534,559 (87.52%) number of supplementary alignments = 11,743 (0.67%) number of secondary alignments = 0 number of mapped bases = 102,609,298 bp number of sequenced bases = 102,566,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,189 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0266 >>>>>>> ACTG content number of A's = 28,551,425 bp (27.84%) number of C's = 18,677,524 bp (18.21%) number of T's = 32,856,553 bp (32.03%) number of G's = 22,479,841 bp (21.92%) number of N's = 1,352 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 715,736 number of insertions = 7,165 mapped reads with insertion percentage = 0.46% number of deletions = 24,844 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.3725X There is a 2.74% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 7020625 0.028166930825821293 0.8040023088732502 chr2 243199373 10304582 0.04237092338227369 0.3968839633846223 chr3 198022430 6802425 0.034351790350214365 0.21600263427864425 chr4 191154276 7233768 0.03784256440070428 0.23397620928766316 chr5 180915260 5904691 0.032637882509192424 0.21221949775191412 chr6 171115067 5849636 0.03418539408923003 0.2444539894510334 chr7 159138663 5683207 0.03571229576058459 0.43794788396246687 chr8 146364022 4806217 0.032837420933950555 0.5096421610672361 chr9 141213431 4591694 0.032515986386592366 0.3129191030566516 chr10 135534747 4232606 0.031228936443877378 0.2878502857016231 chr11 135006516 5299826 0.03925607561045424 0.2973260844107948 chr12 133851895 4713754 0.03521619174685573 0.22461446858889425 chr13 115169878 3281115 0.028489350314324376 0.19750339892605545 chr14 107349540 3296079 0.030704174419378043 0.21665731414833778 chr15 102531392 2888146 0.028168407193769493 0.19956421026606952 chr16 90354753 2895510 0.032046017545972375 0.22232538867537358 chr17 81195210 2686967 0.03309267874299481 0.2328016519351711 chr18 78077248 2587872 0.0331450206851553 0.5593319824829671 chr19 59128983 2282545 0.038602811754770074 0.5177121277508043 chr20 63025520 2008524 0.03186842409233593 0.22163088386429194 chr21 48129895 1359811 0.02825293925947688 0.20602996022170475 chr22 51304566 1089658 0.021239006290395285 0.16652988277976805 chrMT 16571 32172 1.9414640033793977 1.7950127082715424 chrX 155270560 5521116 0.035558034955242 0.2488828754327657 chrY 59373566 236752 0.003987498409645801 0.09317820680095318