BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971308.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,330,949 number of mapped reads = 6,134,910 (83.69%) number of secondary alignments = 0 number of mapped bases = 241,639,024 bp number of sequenced bases = 241,615,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 340,960 duplication rate = 4.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1674 >>>>>>> ACTG content number of A's = 70,200,505 bp (29.05%) number of C's = 49,243,472 bp (20.38%) number of T's = 71,831,489 bp (29.73%) number of G's = 50,326,398 bp (20.83%) number of N's = 13,470 bp (0.01%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 736,521 number of insertions = 9,072 mapped reads with insertion percentage = 0.15% number of deletions = 19,256 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0781X std coverageData = 0.577X There is a 6.53% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 18935021 0.07596779869206424 1.0878318606496433 chr2 243199373 20150503 0.08285590029049951 0.5004107785516119 chr3 198022430 17035069 0.0860259567565149 0.339630183290446 chr4 191154276 16531747 0.08648379385455128 0.369368954975572 chr5 180915260 15296572 0.08455103234519852 0.33984836024824716 chr6 171115067 14219703 0.08310023920921002 0.38593220206497164 chr7 159138663 13388196 0.08412912203491367 0.8260477758792212 chr8 146364022 12483061 0.08528776969520556 0.8611975808562887 chr9 141213431 10156025 0.07191968163424908 0.5127908643210738 chr10 135534747 11385146 0.0840016767065644 0.6291364603299455 chr11 135006516 11010765 0.08155728572389795 0.45511393345498574 chr12 133851895 10519740 0.07859238750411415 0.33702530110695755 chr13 115169878 8087722 0.0702242820818131 0.30153568743482956 chr14 107349540 7348067 0.06844991604062765 0.3794391176734265 chr15 102531392 6753130 0.06586402338124893 0.29316769521663166 chr16 90354753 6468051 0.07158506647680173 0.3862676608858633 chr17 81195210 5780960 0.07119828866752115 0.3529708200600711 chr18 78077248 6441465 0.08250117883253262 0.9018001171481498 chr19 59128983 4343180 0.07345264165967474 1.0042777123744882 chr20 63025520 4604291 0.07305439130053984 0.32575781222104083 chr21 48129895 3039169 0.06314514087346336 0.349519548926237 chr22 51304566 2429268 0.04734993762543474 0.2581458644026604 chrMT 16571 8152 0.4919437571661336 0.8717699069124456 chrX 155270560 14307848 0.09214784824631275 0.4185437132935221 chrY 59373566 916173 0.015430654779940284 0.23158157590368042