BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716444.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 = 588,808 number of mapped reads = 538,835 (91.51%) number of supplementary alignments = 8,451 (1.44%) number of secondary alignments = 0 number of mapped bases = 42,874,830 bp number of sequenced bases = 42,855,706 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,185 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.289 >>>>>>> ACTG content number of A's = 11,275,104 bp (26.31%) number of C's = 8,130,420 bp (18.97%) number of T's = 13,048,592 bp (30.45%) number of G's = 10,399,027 bp (24.27%) number of N's = 2,563 bp (0.01%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 352,321 number of insertions = 4,196 mapped reads with insertion percentage = 0.77% number of deletions = 10,872 mapped reads with deletion percentage = 1.99% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 0.1848X There is a 1.29% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3410890 0.013684579746744141 0.27775861623028136 chr2 243199373 3669808 0.015089709955790058 0.2414045649122337 chr3 198022430 2857522 0.01443029458834537 0.1260141534896286 chr4 191154276 2790382 0.014597539005614502 0.1301068844172917 chr5 180915260 2601381 0.014379002633608685 0.1267023885625702 chr6 171115067 2475400 0.014466288932931897 0.13906751455191108 chr7 159138663 2380641 0.014959538776569966 0.2259286667959324 chr8 146364022 2176674 0.014871646530730073 0.22570182909783087 chr9 141213431 1850910 0.013107181001784455 0.19471661066646556 chr10 135534747 2022703 0.014923870407933105 0.176178434022741 chr11 135006516 1932431 0.014313612833324283 0.187534490515057 chr12 133851895 1944980 0.01453083648909117 0.12705233164861107 chr13 115169878 1365704 0.011858170067697736 0.11330612771582561 chr14 107349540 1302784 0.012135906683903816 0.13398565668139417 chr15 102531392 1217293 0.011872393188614858 0.11461424188151453 chr16 90354753 1211479 0.013408027356347264 0.12989539700437783 chr17 81195210 1134878 0.013977154563674384 0.13370911526405088 chr18 78077248 1204248 0.015423801822523254 0.37210309248925943 chr19 59128983 864940 0.014628020914887036 0.22130002660956716 chr20 63025520 853518 0.0135424190074116 0.12785638368748503 chr21 48129895 551949 0.011467903680238653 0.11633611640186595 chr22 51304566 451847 0.008807149835357735 0.09751742858890615 chrMT 16571 1305 0.07875203669060407 0.2974585683933354 chrX 155270560 2492350 0.01605165847279742 0.15741043454801665 chrY 59373566 108813 0.0018326842622186446 0.062117385851699985