BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716379.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 = 1,259,399 number of mapped reads = 1,117,422 (88.73%) number of supplementary alignments = 4,304 (0.34%) number of secondary alignments = 0 number of mapped bases = 64,489,530 bp number of sequenced bases = 64,470,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,871 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8616 >>>>>>> ACTG content number of A's = 15,977,859 bp (24.78%) number of C's = 12,592,203 bp (19.53%) number of T's = 19,209,850 bp (29.8%) number of G's = 16,690,152 bp (25.89%) number of N's = 434 bp (0%) GC percentage = 45.42% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 347,104 number of insertions = 3,896 mapped reads with insertion percentage = 0.35% number of deletions = 11,873 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.86% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.1891X There is a 1.93% of reference with a coverageData >= 1X There is a 0.11% 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 5486102 0.022010384479643885 0.2303870689100771 chr2 243199373 4981214 0.020482018265729658 0.25173480255971925 chr3 198022430 3658494 0.018475149507053316 0.1460917546284646 chr4 191154276 3884730 0.020322485488109093 0.15756144422422683 chr5 180915260 3608081 0.019943486248755356 0.1481676282168288 chr6 171115067 3407302 0.01991234354599528 0.1707709865179989 chr7 159138663 3641599 0.022883182071223005 0.26344499028360296 chr8 146364022 3329896 0.022750782292659325 0.182156310606987 chr9 141213431 2156391 0.015270438404686875 0.14564560513015692 chr10 135534747 2813685 0.020759879383550256 0.23892984833761108 chr11 135006516 2318342 0.017172074864890224 0.16252874465127706 chr12 133851895 3221262 0.02406586772641508 0.16505767747085046 chr13 115169878 1883594 0.01635491877485535 0.13508435011635525 chr14 107349540 2179699 0.02030468877649592 0.1548475748198589 chr15 102531392 2355316 0.02297165730472088 0.16134009135979407 chr16 90354753 2312146 0.025589644409741236 0.178545423066755 chr17 81195210 3055988 0.037637540441117154 0.21473890069126308 chr18 78077248 1179478 0.015106551911255888 0.21602968269887615 chr19 59128983 1805987 0.030543177108255017 0.24199541760780355 chr20 63025520 2159101 0.03425756741078852 0.20351081163159485 chr21 48129895 799635 0.016614102316242326 0.14547140986815363 chr22 51304566 631220 0.012303388357285783 0.11724429864851203 chrMT 16571 12053 0.7273550178021846 1.0560934674595606 chrX 155270560 3423559 0.022048989840701288 0.1643058688280483 chrY 59373566 184656 0.00311007090259662 0.09282743915556699