BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714264.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 442,060 number of mapped reads = 45,012 (10.18%) number of supplementary alignments = 1,137 (0.26%) number of secondary alignments = 0 number of mapped bases = 4,509,138 bp number of sequenced bases = 4,458,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,272 duplication rate = 37.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.727 >>>>>>> ACTG content number of A's = 643,045 bp (14.42%) number of C's = 416,592 bp (9.34%) number of T's = 559,637 bp (12.55%) number of G's = 2,839,173 bp (63.68%) number of N's = 98 bp (0%) GC percentage = 73.02% >>>>>>> Mismatches and indels general error rate = 0.0355 number of mismatches = 136,164 number of insertions = 4,421 mapped reads with insertion percentage = 7.68% number of deletions = 8,011 mapped reads with deletion percentage = 17.12% homopolymer indels = 37.69% >>>>>>> Coverage mean coverageData = 0.0015X std coverageData = 2.9532X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 127719 5.124119630578574E-4 0.1309112103652091 chr2 243199373 2589647 0.010648247024880281 10.521473988925818 chr3 198022430 100887 5.094725885345413E-4 0.10158744983841404 chr4 191154276 77513 4.054996917777555E-4 0.08518404345967488 chr5 180915260 109497 6.052391600354774E-4 0.12526941526238075 chr6 171115067 111404 6.510472862100449E-4 0.17904624022596977 chr7 159138663 110351 6.934267130295044E-4 0.23715613700915517 chr8 146364022 158088 0.0010801015019934338 0.30415795646902505 chr9 141213431 54032 3.826264939345607E-4 0.07723397415841382 chr10 135534747 82299 6.072169817825388E-4 0.18730011367847202 chr11 135006516 84199 6.236661940079988E-4 0.14709670413401466 chr12 133851895 101491 7.582335685273637E-4 0.15593482455887567 chr13 115169878 44272 3.844060683992389E-4 0.08289837484343415 chr14 107349540 60377 5.624337095436086E-4 0.1454245929728622 chr15 102531392 50930 4.967259198041513E-4 0.10898255786140976 chr16 90354753 25808 2.8562968901038333E-4 0.05167576475701667 chr17 81195210 40083 4.936621261278836E-4 0.14888327645635405 chr18 78077248 42618 5.458440338470946E-4 0.11183121854035566 chr19 59128983 17221 2.912446506986261E-4 0.10401081128749529 chr20 63025520 36184 5.741166435437582E-4 0.10185087778547855 chr21 48129895 17316 3.597763926141954E-4 0.08917317247996934 chr22 51304566 5509 1.0737835692830927E-4 0.026466807204956897 chrMT 16571 14556 0.8784020276386458 7.612013409222528 chrX 155270560 440066 0.0028341882711056107 0.31231320624079684 chrY 59373566 7071 1.190934026095047E-4 0.028781975666482783