BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237851.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,127,604 number of mapped reads = 1,754,974 (82.49%) number of supplementary alignments = 9,924 (0.47%) number of secondary alignments = 0 number of mapped bases = 113,197,410 bp number of sequenced bases = 113,146,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,918 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.465 >>>>>>> ACTG content number of A's = 30,769,374 bp (27.19%) number of C's = 19,769,312 bp (17.47%) number of T's = 36,660,333 bp (32.4%) number of G's = 25,849,057 bp (22.85%) number of N's = 98,181 bp (0.09%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 854,012 number of insertions = 8,765 mapped reads with insertion percentage = 0.5% number of deletions = 31,051 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.3713X There is a 3.14% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 12979611 0.05207453826163185 0.7640420660002261 chr2 243199373 14472805 0.059510042404591235 0.35204656993884015 chr3 198022430 10670535 0.05388548660876447 0.30484990921802535 chr4 191154276 4955514 0.025924159813197168 0.2049117775177985 chr5 180915260 7393611 0.04086781291970616 0.22809538502018833 chr6 171115067 6417685 0.03750508422499113 0.24080079150723302 chr7 159138663 5572579 0.03501712842717549 0.37235750524018274 chr8 146364022 3472853 0.02372750456392897 0.2462043018773503 chr9 141213431 3705012 0.026236966085754265 0.2606296717256525 chr10 135534747 5337403 0.0393803295327655 0.7464278989224676 chr11 135006516 3889547 0.028810068693276996 0.24933193891159713 chr12 133851895 5199253 0.0388433275449705 0.22295427539312315 chr13 115169878 1796904 0.015602204597281939 0.14022872873480285 chr14 107349540 2655158 0.02473376224993605 0.1859642875788379 chr15 102531392 3393797 0.03310007729145041 0.20410705589363048 chr16 90354753 2647515 0.029301336256212222 0.24466714550607446 chr17 81195210 1379016 0.01698395755119052 0.164390369783901 chr18 78077248 1856168 0.023773481360408605 0.5129954172543372 chr19 59128983 2597600 0.04393107860488654 0.4906606674707193 chr20 63025520 2782231 0.04414451479337259 0.23841593197054464 chr21 48129895 1938883 0.04028438042509754 0.24114708155939046 chr22 51304566 1251542 0.02439435897381921 0.1742225671564323 chrMT 16571 29261 1.7657956671293222 1.739217452737018 chrX 155270560 6470310 0.04167119639421665 0.2743058485807956 chrY 59373566 332617 0.005602105826016918 0.15417914130620664