BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080711.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 = 2,113,520 number of mapped reads = 1,940,655 (91.82%) number of supplementary alignments = 13,080 (0.62%) number of secondary alignments = 0 number of mapped bases = 132,494,449 bp number of sequenced bases = 132,445,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,062 duplication rate = 4.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.578 >>>>>>> ACTG content number of A's = 37,403,691 bp (28.24%) number of C's = 24,487,744 bp (18.49%) number of T's = 42,143,138 bp (31.82%) number of G's = 28,409,413 bp (21.45%) number of N's = 1,950 bp (0%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,019,969 number of insertions = 9,252 mapped reads with insertion percentage = 0.47% number of deletions = 27,561 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.3106X There is a 3.44% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 16445828 0.06598109137710031 0.42422349065534315 chr2 243199373 9062732 0.03726461909916191 0.3297714236400433 chr3 198022430 8619382 0.043527301427419104 0.2475624345355752 chr4 191154276 5778092 0.030227375086288942 0.209920120763326 chr5 180915260 4508361 0.024919738666600043 0.1860902901789275 chr6 171115067 7836872 0.045798842482994206 0.30646271048274076 chr7 159138663 8345862 0.052443962030773124 0.6007059380902312 chr8 146364022 16215168 0.11078657021327276 0.4647584083846346 chr9 141213431 4189562 0.02966829692000048 0.24344485247858325 chr10 135534747 6569331 0.048469718248708576 0.30373607235757333 chr11 135006516 5892473 0.043645841508864656 0.2630595255656428 chr12 133851895 4377293 0.032702510487430905 0.21612765405639958 chr13 115169878 2883667 0.025038378524634714 0.18810646640056383 chr14 107349540 1532954 0.014280023929306078 0.14774071112334725 chr15 102531392 2181191 0.02127339693193671 0.1726483093834902 chr16 90354753 3361651 0.03720502672394002 0.23600010643804992 chr17 81195210 2125591 0.02617877335374833 0.19763411166476869 chr18 78077248 4436419 0.056820893584773886 0.3691863792769121 chr19 59128983 2186457 0.03697775420896382 0.30551650181595646 chr20 63025520 3401532 0.05397070900803357 0.28014473303248394 chr21 48129895 1943336 0.04037690088457496 0.24398213155819246 chr22 51304566 1308046 0.025495703442847562 0.18903287171322583 chrMT 16571 29742 1.7948222798865487 1.7567368141591528 chrX 155270560 8980178 0.057835677284863274 0.29507531053725683 chrY 59373566 282729 0.004761866585544146 0.09242521316384887