BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237326.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 = 2,866,743 number of mapped reads = 2,621,138 (91.43%) number of supplementary alignments = 30,695 (1.07%) number of secondary alignments = 0 number of mapped bases = 162,883,388 bp number of sequenced bases = 162,810,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 562,876 duplication rate = 17.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2891 >>>>>>> ACTG content number of A's = 41,772,190 bp (25.66%) number of C's = 28,338,336 bp (17.41%) number of T's = 54,120,129 bp (33.24%) number of G's = 38,562,340 bp (23.69%) number of N's = 17,583 bp (0.01%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 934,633 number of insertions = 11,812 mapped reads with insertion percentage = 0.45% number of deletions = 41,687 mapped reads with deletion percentage = 1.57% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.5669X There is a 3.02% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 9093311 0.03648260118076095 0.3774036147727001 chr2 243199373 14456084 0.05944128811549197 1.2688147044687008 chr3 198022430 10340871 0.05222070550290692 0.36054675939446473 chr4 191154276 7382479 0.03862052764124408 0.4392073398079505 chr5 180915260 7457826 0.041222758102329234 0.32050670170478734 chr6 171115067 13887157 0.08115683348912811 0.596288989101946 chr7 159138663 12146163 0.07632440018677296 0.49626242191909425 chr8 146364022 12736965 0.08702251295062116 0.7240751016431424 chr9 141213431 7460699 0.05283278613915981 0.44162201593354805 chr10 135534747 7188709 0.053039601719255064 0.5918461088474173 chr11 135006516 5721609 0.042380243335810544 0.3622173995815929 chr12 133851895 6767999 0.050563340922442676 0.3603830042718362 chr13 115169878 5386768 0.04677236872648246 0.3887966905879511 chr14 107349540 8746246 0.08147446183747038 0.4569002610462199 chr15 102531392 3040703 0.02965631247842612 0.29204705468677256 chr16 90354753 3917905 0.04336136030386802 0.3532032792571409 chr17 81195210 4143486 0.051031163045209195 0.3815542875102614 chr18 78077248 4894701 0.06269049083287362 0.9337822611375113 chr19 59128983 1447443 0.024479416464849395 0.3304616652403258 chr20 63025520 3823094 0.06065945985054943 0.4023032531815172 chr21 48129895 1789403 0.03717861840338525 0.3595162102267943 chr22 51304566 304105 0.005927445132271463 0.1101925466795731 chrMT 16571 23437 1.414338301852634 2.2104460846148712 chrX 155270560 10234764 0.06591567648110498 0.429114956577015 chrY 59373566 491461 0.008277437807929543 0.33978634150374626