BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716283.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 = 1,352,877 number of mapped reads = 1,237,849 (91.5%) number of supplementary alignments = 5,083 (0.38%) number of secondary alignments = 0 number of mapped bases = 71,315,344 bp number of sequenced bases = 71,296,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,459 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2694 >>>>>>> ACTG content number of A's = 17,480,482 bp (24.52%) number of C's = 14,423,672 bp (20.23%) number of T's = 21,734,670 bp (30.49%) number of G's = 17,655,747 bp (24.76%) number of N's = 1,531 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 347,950 number of insertions = 3,533 mapped reads with insertion percentage = 0.28% number of deletions = 11,123 mapped reads with deletion percentage = 0.89% homopolymer indels = 42.36% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.1944X There is a 2.12% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 8054569 0.03231514115264732 0.28211513934234267 chr2 243199373 5960099 0.024507049201973066 0.22519379370409737 chr3 198022430 4673910 0.023602932253684594 0.1642409843074567 chr4 191154276 4529600 0.02369604329437025 0.17295464917613848 chr5 180915260 3523162 0.019474100747499133 0.15003064322412268 chr6 171115067 3782883 0.022107246698503762 0.16750485793985043 chr7 159138663 3101788 0.01949110254872507 0.17516763938060742 chr8 146364022 4486717 0.030654507430794706 0.20791841745225403 chr9 141213431 2597468 0.018393916085786485 0.19185828262074922 chr10 135534747 3396191 0.025057714535741894 0.2078612111701191 chr11 135006516 2211116 0.016377846532977712 0.17197076272363088 chr12 133851895 3212290 0.023998838417640632 0.16691380703158334 chr13 115169878 2206935 0.019162432385315196 0.14666007299732636 chr14 107349540 2500930 0.023297072348889433 0.1706735674377142 chr15 102531392 2033363 0.019831614107023925 0.15028225335623183 chr16 90354753 2149437 0.023788864765088784 0.17617794057963676 chr17 81195210 1601073 0.019718810998826164 0.1541458733626477 chr18 78077248 1730237 0.022160578713020213 0.3329277554347148 chr19 59128983 1381703 0.023367609755777466 0.2202947852550823 chr20 63025520 2238274 0.03551377283360772 0.20776420817086216 chr21 48129895 920804 0.01913164364892132 0.15810777739498078 chr22 51304566 855670 0.016678242634388527 0.13750677220965796 chrMT 16571 384 0.023173013095166253 0.1571235238924841 chrX 155270560 3967871 0.025554561019165513 0.18497526454910831 chrY 59373566 198870 0.0033494703686822516 0.08030383235821234