BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506015.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 9,717,352 number of mapped reads = 6,798,487 (69.96%) number of supplementary alignments = 332 (0%) number of secondary alignments = 0 number of mapped bases = 317,224,785 bp number of sequenced bases = 317,154,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 467,202 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3874 >>>>>>> ACTG content number of A's = 93,914,371 bp (29.61%) number of C's = 62,991,940 bp (19.86%) number of T's = 94,407,968 bp (29.77%) number of G's = 64,751,675 bp (20.42%) number of N's = 1,088,231 bp (0.34%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,570,223 number of insertions = 14,681 mapped reads with insertion percentage = 0.22% number of deletions = 50,297 mapped reads with deletion percentage = 0.74% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.1025X std coverageData = 0.8337X There is a 7.58% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 32318450 0.1296624653143793 1.8243769863043777 chr2 243199373 19390975 0.07973283302831541 0.6086848132008056 chr3 198022430 20563646 0.10384503412062966 0.4169424177120394 chr4 191154276 13436773 0.07029281939787735 0.35414829173649914 chr5 180915260 22214222 0.12278799477722332 0.455851652024933 chr6 171115067 21737983 0.12703722343748958 0.6227922464511707 chr7 159138663 19879789 0.1249211764459778 1.2196228826514508 chr8 146364022 18558436 0.1267964336208252 1.1002458016735461 chr9 141213431 14557025 0.10308527239168915 0.5831345800933372 chr10 135534747 9713510 0.07166804243933107 0.8659884732541233 chr11 135006516 15986034 0.1184093514419704 0.6338444862858819 chr12 133851895 9126343 0.06818239667058879 0.3644922067515204 chr13 115169878 9688363 0.08412236921879869 0.369612945481208 chr14 107349540 11644010 0.10846818719484033 1.018914240949508 chr15 102531392 10575554 0.10314454718414434 0.4086381718466055 chr16 90354753 9655942 0.10686700676388325 0.5302639952191046 chr17 81195210 5102795 0.06284601025109733 0.36690296077251816 chr18 78077248 9826392 0.1258547432409503 1.0048412088831946 chr19 59128983 7574169 0.1280957090028083 1.2595484526453693 chr20 63025520 7531708 0.11950251263297788 0.4645489368709375 chr21 48129895 4493319 0.09335817167272024 0.44177447429101363 chr22 51304566 2340671 0.04562305429111319 0.268901187369249 chrMT 16571 30297 1.8283145253756563 2.0245786410116304 chrX 155270560 20372441 0.13120607667029732 0.5607110950619184 chrY 59373566 905938 0.015258271669247557 0.2200665064855755