BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080790.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 = 2,279,297 number of mapped reads = 2,049,891 (89.94%) number of supplementary alignments = 20,069 (0.88%) number of secondary alignments = 0 number of mapped bases = 135,312,922 bp number of sequenced bases = 135,266,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,957 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1904 >>>>>>> ACTG content number of A's = 38,743,992 bp (28.64%) number of C's = 25,889,233 bp (19.14%) number of T's = 41,482,168 bp (30.67%) number of G's = 29,148,104 bp (21.55%) number of N's = 2,608 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,021,963 number of insertions = 10,309 mapped reads with insertion percentage = 0.5% number of deletions = 29,725 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.73% >>>>>>> Coverage mean coverageData = 0.0437X std coverageData = 0.3245X There is a 3.67% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% 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 16644971 0.06678005829321484 0.5002164590493503 chr2 243199373 10091179 0.041493441679226695 0.3680481883909076 chr3 198022430 7049190 0.03559793706197828 0.2172469595618786 chr4 191154276 8432523 0.044113703216348665 0.248178292959391 chr5 180915260 10402594 0.05749981510680746 0.2777074326111692 chr6 171115067 10001410 0.05844844744151022 0.33780464659839965 chr7 159138663 9091056 0.05712663301689295 0.45009177198452993 chr8 146364022 5917640 0.04043097421851389 0.3953222565546319 chr9 141213431 4947962 0.03503889088283677 0.28692094373812393 chr10 135534747 5701456 0.04206637874197677 0.29656435422568006 chr11 135006516 5035370 0.03729723682373968 0.267845745096219 chr12 133851895 5647793 0.042194344727058214 0.23770460377563876 chr13 115169878 6127750 0.05320618643010111 0.26853477650679247 chr14 107349540 3857361 0.0359327203451454 0.23079167562107197 chr15 102531392 3317372 0.03235469581842798 0.21786210562829791 chr16 90354753 2717660 0.030077665089738 0.21753389849160465 chr17 81195210 3199362 0.039403334260727944 0.24095217076459155 chr18 78077248 1761802 0.022564857818759186 0.5586741992998078 chr19 59128983 1895974 0.03206505344426438 0.35976180875429625 chr20 63025520 2502288 0.03970277436822418 0.2353228933095426 chr21 48129895 2284779 0.047471098783822406 0.25743852215592655 chr22 51304566 1093600 0.021315841556870396 0.16586242525761627 chrMT 16571 17335 1.0461046406372578 1.2615256642729706 chrX 155270560 7283231 0.046906709166245036 0.2660533459605151 chrY 59373566 291264 0.004905617425774965 0.1076253715506421