BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354861.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 21,083,160 number of mapped reads = 20,782,259 (98.57%) number of supplementary alignments = 759,057 (3.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,418,619 number of mapped paired reads (second in pair) = 10,363,640 number of mapped paired reads (both in pair) = 20,700,828 number of mapped paired reads (singletons) = 81,431 number of mapped bases = 2,668,940,627 bp number of sequenced bases = 2,667,561,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,074,118 duplication rate = 55.47% >>>>>>> Insert size mean insert size = 343,515.4429 std insert size = 6,736,308.7835 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.5231 >>>>>>> ACTG content number of A's = 740,416,733 bp (27.76%) number of C's = 570,909,548 bp (21.4%) number of T's = 750,126,775 bp (28.12%) number of G's = 606,095,037 bp (22.72%) number of N's = 13,180 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 19,249,115 number of insertions = 443,705 mapped reads with insertion percentage = 1.95% number of deletions = 437,477 mapped reads with deletion percentage = 1.97% homopolymer indels = 38.41% >>>>>>> Coverage mean coverageData = 0.8621X std coverageData = 35.6199X There is a 25.1% of reference with a coverageData >= 1X There is a 16.56% of reference with a coverageData >= 2X There is a 10.06% of reference with a coverageData >= 3X There is a 7.72% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 2.63% of reference with a coverageData >= 7X There is a 2.24% of reference with a coverageData >= 8X There is a 1.45% of reference with a coverageData >= 9X There is a 1.24% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.69% of reference with a coverageData >= 12X There is a 0.45% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 215136599 0.8631336529348106 30.80983669396209 chr2 243199373 247468727 1.0175549547983416 115.43385593245934 chr3 198022430 169127664 0.8540833682325785 2.554328523887366 chr4 191154276 179986292 0.9415760702104304 18.70851506034515 chr5 180915260 155446626 0.8592234065827283 2.2112739984747214 chr6 171115067 143968182 0.8413530411088814 3.76679556344231 chr7 159138663 142984452 0.8984897152240119 17.161821401128048 chr8 146364022 132833592 0.907556311892003 12.094543977741445 chr9 141213431 112797175 0.7987708690400702 14.79551692671339 chr10 135534747 154128494 1.1371880452176593 34.95749643513895 chr11 135006516 122683950 0.9087261388183664 5.870276350727884 chr12 133851895 114696789 0.8568932774541593 2.1620860189249087 chr13 115169878 79763830 0.692575449285446 1.898399264982889 chr14 107349540 79031830 0.7362102343428766 4.896852256158387 chr15 102531392 71848611 0.7007474452312127 1.9040444933599565 chr16 90354753 83828029 0.927765570893653 6.330287533892168 chr17 81195210 74932445 0.9228678021770004 5.401133265983989 chr18 78077248 75292887 0.9643383819060836 17.23643448144016 chr19 59128983 54938677 0.9291327909360457 19.264769926575823 chr20 63025520 57282589 0.9088792762043059 6.5134974751092 chr21 48129895 38466108 0.7992144591215086 10.520155207932149 chr22 51304566 34471621 0.6719016198285354 3.087602904937695 chrMT 16571 14445769 871.749984913403 295.72579341934386 chrX 155270560 71810131 0.46248387975157684 2.2968121031052595 chrY 59373566 41569558 0.7001357809635352 22.861671917124784