BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472554.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,390,276 number of mapped reads = 12,152,396 (98.08%) number of supplementary alignments = 55,544 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,095,696 number of mapped paired reads (second in pair) = 6,056,700 number of mapped paired reads (both in pair) = 12,052,134 number of mapped paired reads (singletons) = 100,262 number of mapped bases = 1,189,028,524 bp number of sequenced bases = 1,188,879,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,029,991 duplication rate = 44.95% >>>>>>> Insert size mean insert size = 38,628.4122 std insert size = 1,936,356.3533 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 54.927 >>>>>>> ACTG content number of A's = 327,652,545 bp (27.56%) number of C's = 268,556,595 bp (22.59%) number of T's = 324,955,218 bp (27.33%) number of G's = 267,533,032 bp (22.5%) number of N's = 182,484 bp (0.02%) GC percentage = 45.09% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 7,236,848 number of insertions = 64,083 mapped reads with insertion percentage = 0.52% number of deletions = 59,189 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.3841X std coverageData = 12.616X There is a 3.97% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 130539298 0.5237270722787888 14.552259271434117 chr2 243199373 78550566 0.3229883573754115 11.338254865689485 chr3 198022430 119527619 0.6036064651867973 13.955926246516094 chr4 191154276 48984420 0.25625594689809605 9.321883536866578 chr5 180915260 57344444 0.31696852990731683 9.681656913729954 chr6 171115067 86586911 0.506015703456435 16.89706420232413 chr7 159138663 47897202 0.3009777831299236 8.496899479486805 chr8 146364022 58850669 0.4020842567444614 13.084596675650214 chr9 141213431 70798837 0.5013605044409692 13.200303996705724 chr10 135534747 41138105 0.3035244165099596 15.641713043673711 chr11 135006516 55116450 0.40825029511908895 13.097924906433219 chr12 133851895 62188907 0.4646098361177479 16.696491110454215 chr13 115169878 25955032 0.2253630241754706 8.224136251908988 chr14 107349540 40491000 0.3771883885110267 12.632497087326648 chr15 102531392 35206033 0.34336833152523666 12.157478098202093 chr16 90354753 38638814 0.4276345484559069 11.848788641248891 chr17 81195210 50856243 0.6263453595353716 16.203442235517556 chr18 78077248 16363597 0.20958214357145374 7.111046345738527 chr19 59128983 31611783 0.5346241622319126 22.171937688307036 chr20 63025520 25345482 0.40214633691241264 11.081480779867324 chr21 48129895 4362893 0.09064829665637127 3.1682559431304513 chr22 51304566 9426596 0.18373795423978442 5.645611487715855 chrMT 16571 2547 0.15370225092028242 0.5830631246963984 chrX 155270560 50870743 0.32762645410694724 10.033752866471701 chrY 59373566 2374333 0.039989732130962116 2.062552799810277