BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004114.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 = 1,645,475 number of mapped reads = 1,505,502 (91.49%) number of supplementary alignments = 11,345 (0.69%) number of secondary alignments = 0 number of mapped bases = 101,057,339 bp number of sequenced bases = 101,011,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,489 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0889 >>>>>>> ACTG content number of A's = 28,420,443 bp (28.14%) number of C's = 19,176,417 bp (18.98%) number of T's = 30,667,917 bp (30.36%) number of G's = 22,724,423 bp (22.5%) number of N's = 22,165 bp (0.02%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 856,810 number of insertions = 8,942 mapped reads with insertion percentage = 0.59% number of deletions = 27,416 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.2837X There is a 2.91% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7415822 0.029752471509388936 0.4063530063306907 chr2 243199373 4711939 0.01937479912828558 0.3557940860477193 chr3 198022430 8967814 0.04528685967544182 0.23145874565563315 chr4 191154276 4135162 0.02163258958434181 0.1742672403510964 chr5 180915260 6320569 0.034936627236419965 0.2054507697762519 chr6 171115067 6790713 0.039685067592557466 0.23378732315274733 chr7 159138663 5872551 0.03690210090554801 0.29326058094476276 chr8 146364022 5811664 0.03970691649891939 0.34846294493265667 chr9 141213431 5183503 0.03670686961780569 0.3298818563438395 chr10 135534747 3299220 0.024342244870977626 0.28213015428023547 chr11 135006516 3754969 0.027813242732669288 0.23349691616090174 chr12 133851895 5149227 0.03846958610485118 0.21867735148589856 chr13 115169878 2665180 0.02314129394145924 0.16469018805629665 chr14 107349540 2774566 0.025846091189584978 0.20344168151634412 chr15 102531392 3989958 0.03891450142411019 0.21538095662962156 chr16 90354753 2320795 0.02568536709961456 0.21738751112138519 chr17 81195210 3421756 0.042142338199507086 0.2363162754892434 chr18 78077248 3965698 0.050791979758302956 0.5857518323744345 chr19 59128983 1686785 0.028527211435380177 0.31613024230290626 chr20 63025520 2699645 0.04283415670350677 0.23657797299704222 chr21 48129895 1171405 0.024338407553143426 0.19878927273025093 chr22 51304566 525372 0.010240258147783572 0.10810888512029018 chrMT 16571 31797 1.9188341077786495 2.008277475725564 chrX 155270560 8103714 0.05219092402320182 0.26982401930048133 chrY 59373566 287515 0.004842474848150438 0.1134524351563653