BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053618.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,938,923 number of mapped reads = 6,670,765 (84.03%) number of supplementary alignments = 189 (0%) number of secondary alignments = 0 number of mapped bases = 315,549,417 bp number of sequenced bases = 315,485,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,289,646 duplication rate = 14.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0853 >>>>>>> ACTG content number of A's = 92,151,519 bp (29.21%) number of C's = 62,087,930 bp (19.68%) number of T's = 92,775,229 bp (29.41%) number of G's = 68,464,507 bp (21.7%) number of N's = 6,279 bp (0%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,626,728 number of insertions = 12,042 mapped reads with insertion percentage = 0.18% number of deletions = 42,548 mapped reads with deletion percentage = 0.64% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.1019X std coverageData = 0.7373X There is a 5.07% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 25581320 0.10263292383131113 0.7890097145655158 chr2 243199373 26510545 0.1090074561993217 0.9953264923778612 chr3 198022430 21061603 0.10635968359745913 0.6790486696490283 chr4 191154276 20404695 0.10674464326395712 0.7159347372035231 chr5 180915260 19646491 0.10859499082609173 0.6938016472291432 chr6 171115067 18400734 0.10753427107619927 0.7270190966025386 chr7 159138663 17030015 0.10701368654831542 0.7697624941533536 chr8 146364022 15818679 0.10807764629479777 0.7358536399701443 chr9 141213431 13035118 0.09230791935081586 0.6532894056451437 chr10 135534747 14785962 0.10909351533300904 0.7668145132086859 chr11 135006516 14509948 0.10747590879243192 0.7531668201620236 chr12 133851895 14634313 0.10933213160710202 0.7048471126209782 chr13 115169878 10119219 0.0878634168562721 0.6392262889297822 chr14 107349540 9684103 0.09021094082005382 0.6779979641795867 chr15 102531392 9171693 0.08945253566829561 0.6286976490907216 chr16 90354753 9089604 0.10059906865109797 0.6874164115315553 chr17 81195210 8328517 0.10257399420483056 0.6776402885562488 chr18 78077248 8302308 0.10633453679105083 0.7638962649403008 chr19 59128983 5930627 0.10029983096445275 0.7541222377421066 chr20 63025520 6812899 0.10809746591539428 0.7138586265687343 chr21 48129895 4052102 0.08419095865469892 0.682052571908367 chr22 51304566 3553035 0.06925377752927488 0.5412081890852194 chrMT 16571 14543 0.8776175245911532 2.0506318628773563 chrX 155270560 18332175 0.1180660068463719 0.7727539483305242 chrY 59373566 739169 0.012449462779446328 0.2685581985357464