BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124783.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 527,735 number of mapped reads = 527,253 (99.91%) number of supplementary alignments = 244,450 (46.32%) number of secondary alignments = 0 number of mapped bases = 79,017,427 bp number of sequenced bases = 78,977,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 769,318 duplication rate = 16.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9534 >>>>>>> ACTG content number of A's = 21,463,262 bp (27.18%) number of C's = 15,062,725 bp (19.07%) number of T's = 25,581,632 bp (32.39%) number of G's = 16,869,439 bp (21.36%) number of N's = 0 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 598,147 number of insertions = 9,087 mapped reads with insertion percentage = 1.71% number of deletions = 35,778 mapped reads with deletion percentage = 6.57% homopolymer indels = 78.86% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 48.0697X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 89986 3.6102618175623324E-4 0.26585952374056726 chr2 243199373 19344 7.95396787474448E-5 0.009756604118345443 chr3 198022430 19677 9.93675312438091E-5 0.01473454979545222 chr4 191154276 11610 6.0736281933865816E-5 0.00796704701702184 chr5 180915260 13519 7.4725592523262E-5 0.008641196039699593 chr6 171115067 11857 6.92925538813014E-5 0.00987464096727609 chr7 159138663 17231 1.082766417360186E-4 0.010786959312066266 chr8 146364022 61814816 0.4223361394099979 210.62553694967383 chr9 141213431 6995 4.9534948272731934E-5 0.007035416879796947 chr10 135534747 16924630 0.12487299659031348 69.78261857418678 chr11 135006516 14317 1.0604673332952314E-4 0.01127818397080923 chr12 133851895 9832 7.345432053838311E-5 0.008636232562056107 chr13 115169878 4791 4.1599418903612976E-5 0.006446260766866907 chr14 107349540 7420 6.911999809221353E-5 0.01575712305730762 chr15 102531392 8930 8.709527712254214E-5 0.010180789587749548 chr16 90354753 8608 9.52689229309276E-5 0.023337136637663295 chr17 81195210 5051 6.220810316273583E-5 0.007881499353460305 chr18 78077248 4551 5.828842737899779E-5 0.007697118318666208 chr19 59128983 4706 7.958871878449186E-5 0.008915207652821984 chr20 63025520 5445 8.639357517399301E-5 0.009293559462179114 chr21 48129895 2877 5.97757381353107E-5 0.007729902352095037 chr22 51304566 1411 2.750242541765191E-5 0.005329003629139186 chrMT 16571 0 0.0 0.0 chrX 155270560 7328 4.719503813214817E-5 0.007000642669981214 chrY 59373566 2495 4.202206753086045E-5 0.006659171745624709