BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240213.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 = 2,026,785 number of mapped reads = 1,547,633 (76.36%) number of supplementary alignments = 14,286 (0.7%) number of secondary alignments = 0 number of mapped bases = 102,871,462 bp number of sequenced bases = 102,823,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,201 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0607 >>>>>>> ACTG content number of A's = 29,477,356 bp (28.67%) number of C's = 18,925,942 bp (18.41%) number of T's = 32,736,373 bp (31.84%) number of G's = 21,673,992 bp (21.08%) number of N's = 9,884 bp (0.01%) GC percentage = 39.49% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 831,472 number of insertions = 7,485 mapped reads with insertion percentage = 0.48% number of deletions = 27,642 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.3469X There is a 2.52% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 8133349 0.032631208569787275 0.5268453309397046 chr2 243199373 8815427 0.03624773736567158 0.3363083830643523 chr3 198022430 7789517 0.03933653879512538 0.25025919950131587 chr4 191154276 6925724 0.036231070237738236 0.2481674599723448 chr5 180915260 7495308 0.041429937972064936 0.25905180569906494 chr6 171115067 5364335 0.03134928498143299 0.2558906731266207 chr7 159138663 5640509 0.03544398886900288 0.4218259054472574 chr8 146364022 6169507 0.04215180011929434 0.7012999883553944 chr9 141213431 3679158 0.026053881517828146 0.28877990823653893 chr10 135534747 4937449 0.0364293962197015 0.3287464488167374 chr11 135006516 4426763 0.03278925440902423 0.3058886801122861 chr12 133851895 4485579 0.03351150911983727 0.23410795739396895 chr13 115169878 3217418 0.027936280352749875 0.21179858823627187 chr14 107349540 2807838 0.026156031968092273 0.2961925454278778 chr15 102531392 2388222 0.023292593160151382 0.19277342496877758 chr16 90354753 2591527 0.028681689827650795 0.23243229627289172 chr17 81195210 2844320 0.03503063789107756 0.25150283449351063 chr18 78077248 2332310 0.029871826425029734 0.5424753771449783 chr19 59128983 1300544 0.02199503414425376 0.3873667534013794 chr20 63025520 2534411 0.04021245679527912 0.2538046421686416 chr21 48129895 1419497 0.029493041694772033 0.22284339866861555 chr22 51304566 1268080 0.02471670845047203 0.19296242235340305 chrMT 16571 24320 1.4676241626938629 1.8219443193813591 chrX 155270560 6030662 0.038839700198157336 0.2787919138739569 chrY 59373566 249688 0.004205373145348892 0.10982623745533802