BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230333.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 = 2,777,792 number of mapped reads = 2,294,844 (82.61%) number of supplementary alignments = 15,331 (0.55%) number of secondary alignments = 0 number of mapped bases = 150,498,343 bp number of sequenced bases = 150,428,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,823 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4842 >>>>>>> ACTG content number of A's = 41,161,712 bp (27.36%) number of C's = 26,003,451 bp (17.29%) number of T's = 49,536,133 bp (32.93%) number of G's = 33,442,164 bp (22.23%) number of N's = 284,808 bp (0.19%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,378,190 number of insertions = 13,179 mapped reads with insertion percentage = 0.57% number of deletions = 42,297 mapped reads with deletion percentage = 1.82% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.4945X There is a 4.2% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 19406021 0.07785746299103503 1.1240150310591328 chr2 243199373 13523180 0.05560532427852929 0.4225185403843457 chr3 198022430 12498824 0.06311822352649647 0.28433679263915396 chr4 191154276 8037618 0.0420478064534638 0.2471118147823818 chr5 180915260 8407232 0.04647055201424136 0.2425736828500955 chr6 171115067 8624152 0.05039972312899833 0.30611550855406333 chr7 159138663 7204186 0.045269866317778476 0.6139764221792475 chr8 146364022 8949130 0.0611429631251866 0.864743026807318 chr9 141213431 5328537 0.03773392489840432 0.34754118316483534 chr10 135534747 7506330 0.055383067192356215 0.4396994776960871 chr11 135006516 5736848 0.04249311936914215 0.3261805120627077 chr12 133851895 6934308 0.05180582613342904 0.25904628434655685 chr13 115169878 3806531 0.033051445969231645 0.20037361297867867 chr14 107349540 4204953 0.039170666218038754 0.23609126440856354 chr15 102531392 2721728 0.026545314043917398 0.17903168374187353 chr16 90354753 2591766 0.028684334956900384 0.2273421765994865 chr17 81195210 2520854 0.03104683145717586 0.219588443745095 chr18 78077248 3632839 0.04652877878072752 0.694123573968048 chr19 59128983 2996587 0.05067881854149259 0.5790206851928589 chr20 63025520 2048751 0.032506689353772884 0.22099989960504293 chr21 48129895 2158626 0.04485000434760973 0.25766997823755083 chr22 51304566 1017032 0.0198234207848089 0.1669712260510912 chrMT 16571 180064 10.866212057208376 5.926153723310874 chrX 155270560 10086622 0.06496158705166002 0.3231269072247515 chrY 59373566 375624 0.0063264517411671045 0.14078986122868933