BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240045.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 = 1,349,901 number of mapped reads = 1,151,429 (85.3%) number of supplementary alignments = 6,922 (0.51%) number of secondary alignments = 0 number of mapped bases = 75,423,613 bp number of sequenced bases = 75,392,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,429 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3351 >>>>>>> ACTG content number of A's = 21,121,133 bp (28.01%) number of C's = 13,802,985 bp (18.31%) number of T's = 23,168,045 bp (30.73%) number of G's = 17,249,068 bp (22.88%) number of N's = 51,653 bp (0.07%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 710,393 number of insertions = 5,374 mapped reads with insertion percentage = 0.46% number of deletions = 17,928 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2394X There is a 2.23% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 9229781 0.037030122384328984 0.3743888500754199 chr2 243199373 5567319 0.022891995696057984 0.28283544126623184 chr3 198022430 3340934 0.016871492789983438 0.13785938400469533 chr4 191154276 3535127 0.018493580546427326 0.14584458374676626 chr5 180915260 4428648 0.02447912906849317 0.16729309779464252 chr6 171115067 5852578 0.034202587198238946 0.24729838181584723 chr7 159138663 4219514 0.026514700579079266 0.31154978926993215 chr8 146364022 3402238 0.023245043102190784 0.3624312402600126 chr9 141213431 2232994 0.015812900969738496 0.22147979145901084 chr10 135534747 3632970 0.02680471303790459 0.21016404770503855 chr11 135006516 3290765 0.024374860543768126 0.19866833648985918 chr12 133851895 3532563 0.026391580037025252 0.17410581660977653 chr13 115169878 1661056 0.014422660063944845 0.12678059044104517 chr14 107349540 993443 0.009254282785003084 0.13023214736890906 chr15 102531392 1428048 0.013927910000480633 0.12998742304107025 chr16 90354753 2397342 0.026532549981072937 0.19159118774351125 chr17 81195210 1527611 0.018814053193531983 0.14777332586362596 chr18 78077248 4307501 0.05516973395373771 0.45122931386114334 chr19 59128983 1323497 0.02238321941035245 0.25811021354850117 chr20 63025520 2139976 0.03395411890294598 0.20536025887789763 chr21 48129895 2187427 0.04544840581929381 0.23315668977164614 chr22 51304566 424985 0.008283570705967963 0.09530898376784208 chrMT 16571 8920 0.5382897833564662 0.835762926865622 chrX 155270560 4603644 0.029649174962723134 0.19877352546223176 chrY 59373566 154732 0.0026060755724188773 0.06073994259803657