BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082919.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,749,199 number of mapped reads = 3,223,643 (85.98%) number of supplementary alignments = 28,880 (0.77%) number of secondary alignments = 0 number of mapped bases = 220,151,772 bp number of sequenced bases = 220,066,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,913 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2473 >>>>>>> ACTG content number of A's = 63,349,438 bp (28.79%) number of C's = 40,091,697 bp (18.22%) number of T's = 71,282,101 bp (32.39%) number of G's = 45,331,531 bp (20.6%) number of N's = 12,007 bp (0.01%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,955,551 number of insertions = 17,980 mapped reads with insertion percentage = 0.55% number of deletions = 49,785 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0711X std coverageData = 0.5102X There is a 5.57% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17448790 0.07000500111090997 0.9024598170528494 chr2 243199373 23976974 0.09858978542679055 0.6173302050434206 chr3 198022430 17289661 0.08731162929371183 0.3575674759819518 chr4 191154276 13347392 0.06982523372901164 0.32959092636690385 chr5 180915260 12651253 0.06992916462657711 0.3239122380571574 chr6 171115067 12790914 0.07475036666408809 0.4885900410961602 chr7 159138663 11789145 0.07408096045145234 0.4773407957430954 chr8 146364022 18225201 0.12451967875001413 0.8027995479024754 chr9 141213431 7036737 0.04983050797767247 0.45503197450231025 chr10 135534747 8389186 0.06189693924023778 0.3912147710721378 chr11 135006516 9410875 0.06970682066930754 0.435126066876075 chr12 133851895 7119684 0.05319075983197698 0.2899592447447138 chr13 115169878 5547282 0.048166083843554995 0.26537193566180567 chr14 107349540 4870981 0.045374959221995734 0.2952909446378897 chr15 102531392 4232715 0.04128213727947827 0.24409326092973663 chr16 90354753 8192715 0.09067276184131674 0.40332518458614536 chr17 81195210 5432455 0.06690610197325679 0.3688516243586464 chr18 78077248 7306657 0.09358240956443546 0.9393790206163318 chr19 59128983 3607531 0.06101121340104902 0.645963922958248 chr20 63025520 4454434 0.07067667192591191 0.33446768702715474 chr21 48129895 3705031 0.07697982719471962 0.34860305949403375 chr22 51304566 2873593 0.05601047283004012 0.28280350771196044 chrMT 16571 282785 17.065053406553616 10.601934995404967 chrX 155270560 9809326 0.0631756979558778 0.3430790633452608 chrY 59373566 360455 0.0060709676760866945 0.11409819453867079