BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068184.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 = 1,036,768 number of mapped reads = 659,048 (63.57%) number of supplementary alignments = 3,579 (0.35%) number of secondary alignments = 0 number of mapped bases = 39,977,031 bp number of sequenced bases = 39,952,459 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,684 duplication rate = 15.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.587 >>>>>>> ACTG content number of A's = 10,898,169 bp (27.28%) number of C's = 6,942,019 bp (17.38%) number of T's = 13,128,449 bp (32.86%) number of G's = 8,944,342 bp (22.39%) number of N's = 39,480 bp (0.1%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 427,299 number of insertions = 2,808 mapped reads with insertion percentage = 0.42% number of deletions = 13,946 mapped reads with deletion percentage = 2.09% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.2546X There is a 0.58% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 2933710 0.011770121126398317 0.2661586084983074 chr2 243199373 3279657 0.0134854665106394 0.259145093529678 chr3 198022430 2440362 0.01232366454648597 0.23467651151026106 chr4 191154276 2249856 0.011769843955779466 0.23939496273331898 chr5 180915260 2223345 0.012289427658009612 0.2356414408474523 chr6 171115067 2325034 0.013587546910758011 0.25555436826310807 chr7 159138663 2159623 0.013570699660836034 0.28905570884524223 chr8 146364022 1922674 0.013136247376421509 0.2775223799562469 chr9 141213431 1616601 0.011447926649413397 0.23435169273890397 chr10 135534747 2100376 0.015496955920831135 0.2742236938774638 chr11 135006516 1658274 0.012282918255589975 0.2466882096551421 chr12 133851895 2374543 0.01774007756856935 0.2951640914591441 chr13 115169878 1287652 0.01118045814027866 0.23054479133027872 chr14 107349540 1673371 0.015588059343337662 0.2815089732957035 chr15 102531392 1588956 0.015497263511257119 0.28278174188055005 chr16 90354753 1165878 0.012903338909022307 0.2326456279229915 chr17 81195210 1006459 0.012395546486055026 0.23431827499427804 chr18 78077248 991483 0.01269874419754139 0.28627631705839746 chr19 59128983 586419 0.009917623646596459 0.2099813339416548 chr20 63025520 1058764 0.016798972860517455 0.282112756850303 chr21 48129895 560027 0.011635741154224418 0.22318022417573533 chr22 51304566 389502 0.007591955850479273 0.1745945285665899 chrMT 16571 30743 1.8552290145434795 3.207481166522446 chrX 155270560 2246222 0.014466502857979001 0.25562273973290783 chrY 59373566 107500 0.001810570043914829 0.10911369348478936