BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038495.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 67,579,238 number of mapped reads = 67,345,350 (99.65%) number of supplementary alignments = 91,903 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 33,725,844 number of mapped paired reads (second in pair) = 33,619,506 number of mapped paired reads (both in pair) = 67,220,864 number of mapped paired reads (singletons) = 124,486 number of mapped bases = 10,035,088,683 bp number of sequenced bases = 10,033,251,969 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,326,717 duplication rate = 32.99% >>>>>>> Insert size mean insert size = 18,082.7967 std insert size = 1,431,859.4785 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.7017 >>>>>>> ACTG content number of A's = 2,546,749,638 bp (25.38%) number of C's = 2,471,836,223 bp (24.64%) number of T's = 2,566,316,518 bp (25.58%) number of G's = 2,447,379,489 bp (24.39%) number of N's = 970,101 bp (0.01%) GC percentage = 49.03% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 45,609,889 number of insertions = 532,330 mapped reads with insertion percentage = 0.76% number of deletions = 652,032 mapped reads with deletion percentage = 0.94% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 3.2416X std coverageData = 19.8264X There is a 23.44% of reference with a coverageData >= 1X There is a 14.8% of reference with a coverageData >= 2X There is a 9.37% of reference with a coverageData >= 3X There is a 7.21% of reference with a coverageData >= 4X There is a 5.71% of reference with a coverageData >= 5X There is a 4.94% of reference with a coverageData >= 6X There is a 4.41% of reference with a coverageData >= 7X There is a 4.09% of reference with a coverageData >= 8X There is a 3.86% of reference with a coverageData >= 9X There is a 3.7% of reference with a coverageData >= 10X There is a 3.57% of reference with a coverageData >= 11X There is a 3.46% of reference with a coverageData >= 12X There is a 3.37% of reference with a coverageData >= 13X There is a 3.3% of reference with a coverageData >= 14X There is a 3.23% of reference with a coverageData >= 15X There is a 3.16% of reference with a coverageData >= 16X There is a 3.1% of reference with a coverageData >= 17X There is a 3.05% of reference with a coverageData >= 18X There is a 2.99% of reference with a coverageData >= 19X There is a 2.94% of reference with a coverageData >= 20X There is a 2.9% of reference with a coverageData >= 21X There is a 2.85% of reference with a coverageData >= 22X There is a 2.81% of reference with a coverageData >= 23X There is a 2.76% of reference with a coverageData >= 24X There is a 2.72% of reference with a coverageData >= 25X There is a 2.68% of reference with a coverageData >= 26X There is a 2.64% of reference with a coverageData >= 27X There is a 2.61% of reference with a coverageData >= 28X There is a 2.57% of reference with a coverageData >= 29X There is a 2.54% of reference with a coverageData >= 30X There is a 2.5% of reference with a coverageData >= 31X There is a 2.47% of reference with a coverageData >= 32X There is a 2.43% of reference with a coverageData >= 33X There is a 2.4% of reference with a coverageData >= 34X There is a 2.37% of reference with a coverageData >= 35X There is a 2.34% of reference with a coverageData >= 36X There is a 2.31% of reference with a coverageData >= 37X There is a 2.28% of reference with a coverageData >= 38X There is a 2.25% of reference with a coverageData >= 39X There is a 2.22% of reference with a coverageData >= 40X There is a 2.19% of reference with a coverageData >= 41X There is a 2.16% of reference with a coverageData >= 42X There is a 2.13% of reference with a coverageData >= 43X There is a 2.11% of reference with a coverageData >= 44X There is a 2.08% of reference with a coverageData >= 45X There is a 2.05% of reference with a coverageData >= 46X There is a 2.03% of reference with a coverageData >= 47X There is a 2% of reference with a coverageData >= 48X There is a 1.98% of reference with a coverageData >= 49X There is a 1.95% of reference with a coverageData >= 50X There is a 1.93% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 967494747 3.8816141886362643 21.548188488447238 chr2 243199373 742543069 3.053227727688262 20.77588002398273 chr3 198022430 582615013 2.9421667686837294 18.336241497358078 chr4 191154276 413119248 2.1611823530434653 15.726566133312913 chr5 180915260 455986652 2.5204432837782726 16.650425541366516 chr6 171115067 521316297 3.0465832503224277 19.385819745048376 chr7 159138663 514706138 3.234324885587357 21.21877360955563 chr8 146364022 348318938 2.3798125607671534 15.838468555266715 chr9 141213431 401870434 2.845837192356016 18.17349994529976 chr10 135534747 407992302 3.0102413663707948 18.098493571144047 chr11 135006516 567402806 4.202780893923668 23.378634297280698 chr12 133851895 529194739 3.953584213357607 20.936196243993965 chr13 115169878 193324767 1.6786052946934615 13.37015387312531 chr14 107349540 327303531 3.0489514067782686 18.88932131046232 chr15 102531392 358740606 3.498836785518332 19.799561109206145 chr16 90354753 414468803 4.587127840413664 23.02444705202439 chr17 81195210 550070432 6.774666042491916 28.260770811802 chr18 78077248 161239416 2.0651267831571114 14.599498036336504 chr19 59128983 614054884 10.385006689528213 36.81100809565862 chr20 63025520 239102727 3.7937446132931547 21.35685309116963 chr21 48129895 109212234 2.2691143207355844 20.562426419694294 chr22 51304566 211671993 4.125792487943471 21.221188522851474 chrMT 16571 262141 15.819262567135358 7.464963548329633 chrX 155270560 397367911 2.559196740193376 17.707753750112627 chrY 59373566 5708855 0.09615145905165945 2.4493997134855037