BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083611.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 = 1,996,048 number of mapped reads = 1,797,621 (90.06%) number of supplementary alignments = 17,479 (0.88%) number of secondary alignments = 0 number of mapped bases = 118,788,934 bp number of sequenced bases = 118,745,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,999 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2776 >>>>>>> ACTG content number of A's = 31,661,435 bp (26.66%) number of C's = 22,464,022 bp (18.92%) number of T's = 37,030,565 bp (31.18%) number of G's = 27,583,086 bp (23.23%) number of N's = 5,976 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 815,932 number of insertions = 8,573 mapped reads with insertion percentage = 0.47% number of deletions = 26,646 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.2967X There is a 3.15% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% 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 13440201 0.05392243736877189 0.41621551506217414 chr2 243199373 10735422 0.044142474002184205 0.46173325380626995 chr3 198022430 8424427 0.04254279174333938 0.2459498507546896 chr4 191154276 6652990 0.034804295981325575 0.22160553465135546 chr5 180915260 6805893 0.037619231235662486 0.228398287263375 chr6 171115067 8024689 0.04689644892579798 0.31059772083380377 chr7 159138663 8149969 0.051213004095679755 0.4646223279986419 chr8 146364022 8151717 0.055694814125837565 0.2998775420253664 chr9 141213431 3952522 0.02798970304743888 0.22480283266935744 chr10 135534747 4902143 0.03616890213400406 0.24857862495466904 chr11 135006516 4277454 0.031683315196430965 0.22710853114949334 chr12 133851895 3644055 0.02722453051561205 0.19566192722459932 chr13 115169878 3299234 0.028646674436869683 0.20177390729250783 chr14 107349540 2754344 0.025657715906374633 0.19070203437992103 chr15 102531392 2675378 0.026093257370386622 0.20656978861146877 chr16 90354753 4084151 0.04520128564791716 0.2592449720139037 chr17 81195210 2749683 0.033865088839600266 0.22383905035146173 chr18 78077248 2602679 0.03333466620134972 0.3410821685082127 chr19 59128983 3067632 0.05188034436513139 0.354128190696019 chr20 63025520 1720054 0.027291389265808517 0.20144767340314762 chr21 48129895 2095464 0.04353768068681638 0.2511128517346108 chr22 51304566 689658 0.013442429276177875 0.1345751585592059 chrMT 16571 4038 0.24367871582885764 0.6102692043476163 chrX 155270560 5669566 0.036514108018931596 0.2308020656374706 chrY 59373566 215571 0.003630757162202452 0.07256145496638902