BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472807.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,140,082 number of mapped reads = 1,576,857 (73.68%) number of supplementary alignments = 15,363 (0.72%) number of secondary alignments = 0 number of mapped bases = 97,785,471 bp number of sequenced bases = 97,737,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,867 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2907 >>>>>>> ACTG content number of A's = 26,278,037 bp (26.89%) number of C's = 19,613,374 bp (20.07%) number of T's = 28,645,479 bp (29.31%) number of G's = 23,198,867 bp (23.74%) number of N's = 1,807 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 904,221 number of insertions = 7,729 mapped reads with insertion percentage = 0.49% number of deletions = 26,447 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3056X There is a 2.35% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% 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 7968458 0.03196966157207688 0.36045204936255304 chr2 243199373 8262932 0.033975959304796396 0.36051631776566057 chr3 198022430 6091147 0.030759884120197898 0.2460965061801545 chr4 191154276 4907017 0.025670453743864983 0.24395463825636957 chr5 180915260 5529613 0.03056465772981229 0.245938499779586 chr6 171115067 6322054 0.03694621467786936 0.28567213741456 chr7 159138663 5535514 0.03478421833919768 0.420091907694393 chr8 146364022 5285272 0.03611045889405799 0.2991532117859736 chr9 141213431 4303221 0.030473170785008403 0.30796268454556847 chr10 135534747 4844838 0.035746095427469975 0.2994176578394504 chr11 135006516 4014758 0.02973751281752949 0.32136441293953144 chr12 133851895 4477501 0.033451158834919746 0.2810263682510438 chr13 115169878 3752801 0.03258491773343721 0.2537678519118365 chr14 107349540 3044326 0.028359003680872782 0.27452526713061143 chr15 102531392 2872143 0.02801232816579726 0.28072020284877636 chr16 90354753 3025940 0.033489549797120245 0.2747294400974539 chr17 81195210 2700458 0.033258833864707044 0.2844424599590006 chr18 78077248 2053412 0.026299748679666578 0.46288676517804217 chr19 59128983 2109334 0.03567343615566667 0.32314188347764367 chr20 63025520 2955859 0.04689939884668941 0.3195105790806083 chr21 48129895 1460501 0.0303449862086755 0.2608003220011875 chr22 51304566 1153812 0.022489460294820542 0.21957305388139842 chrMT 16571 130669 7.885402208677811 6.282420697419741 chrX 155270560 4600637 0.029629808767354222 0.26547122856771954 chrY 59373566 383254 0.006454960108004966 0.12382509309943035