BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536762.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 21,168,003 number of mapped reads = 20,678,312 (97.69%) number of supplementary alignments = 566 (0%) number of secondary alignments = 0 number of mapped bases = 1,031,307,070 bp number of sequenced bases = 1,031,211,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,140 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6804 >>>>>>> ACTG content number of A's = 321,054,771 bp (31.13%) number of C's = 193,107,618 bp (18.73%) number of T's = 319,451,182 bp (30.98%) number of G's = 197,561,748 bp (19.16%) number of N's = 36,643 bp (0%) GC percentage = 37.88% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 2,033,903 number of insertions = 62,322 mapped reads with insertion percentage = 0.3% number of deletions = 56,832 mapped reads with deletion percentage = 0.27% homopolymer indels = 49.2% >>>>>>> Coverage mean coverageData = 0.3331X std coverageData = 0.6637X There is a 25.14% of reference with a coverageData >= 1X There is a 6.21% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 81203434 0.32579029762979006 0.6733293818345896 chr2 243199373 93666421 0.38514252666268184 0.7013861719664735 chr3 198022430 81950269 0.41384336612776645 0.7249012905740121 chr4 191154276 86116976 0.450510330200513 0.7532786180806853 chr5 180915260 69876123 0.38623675526321 0.7033868988544788 chr6 171115067 72841654 0.4256881365099194 0.7373058512528672 chr7 159138663 56929094 0.357732639741984 0.6824420370392059 chr8 146364022 57775280 0.39473689784228533 0.7103353296788603 chr9 141213431 43940566 0.3111642121350341 0.6505106205334882 chr10 135534747 44108351 0.3254394314101608 0.6432985436257763 chr11 135006516 49382499 0.3657786339734891 0.6995020970221241 chr12 133851895 48176528 0.3599241385413333 0.6826024837492168 chr13 115169878 40888617 0.3550287428454166 0.6829133550124611 chr14 107349540 33995250 0.31667811524856093 0.6548941270119281 chr15 102531392 27174291 0.26503386397016826 0.5976450247330779 chr16 90354753 19199742 0.21249288346790124 0.5288793040828593 chr17 81195210 16122156 0.19856043232106918 0.5068388974872664 chr18 78077248 30277739 0.38779208765145 0.7029038754637633 chr19 59128983 8128625 0.13747276864207186 0.41262152892925374 chr20 63025520 16166116 0.2565011125651958 0.5843434952629121 chr21 48129895 12227452 0.25405108405077553 0.5916891944271357 chr22 51304566 5343419 0.10415094438183144 0.36371679173441407 chrMT 16571 1169 0.07054492788606602 0.2917542987423875 chrX 155270560 30678629 0.19758175020428856 0.4902019692476639 chrY 59373566 5136670 0.08651442630210218 0.3391854853405949