BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708582.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,114,344 number of mapped reads = 5,007,926 (97.92%) number of supplementary alignments = 150 (0%) number of secondary alignments = 0 number of mapped bases = 249,765,680 bp number of sequenced bases = 249,744,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,121 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7152 >>>>>>> ACTG content number of A's = 77,467,621 bp (31.02%) number of C's = 47,222,557 bp (18.91%) number of T's = 77,132,428 bp (30.88%) number of G's = 47,912,148 bp (19.18%) number of N's = 9,525 bp (0%) GC percentage = 38.09% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 364,503 number of insertions = 16,098 mapped reads with insertion percentage = 0.32% number of deletions = 12,603 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0807X std coverageData = 0.2975X There is a 7.42% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.05% 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 19104199 0.07664654524571876 0.29208755743765763 chr2 243199373 21784402 0.0895742523151982 0.311695960347154 chr3 198022430 19379647 0.09786591852246233 0.3263847670758222 chr4 191154276 19803733 0.10360078473996574 0.33500919488400327 chr5 180915260 17362672 0.09597129617479476 0.3222725506414765 chr6 171115067 16545431 0.09669184187035967 0.3243360101475375 chr7 159138663 14276598 0.08971168747345828 0.31361067949191807 chr8 146364022 14005506 0.0956895404254469 0.32288644159866464 chr9 141213431 10092438 0.07146939160482546 0.2802259502832213 chr10 135534747 10325783 0.07618550392837639 0.2879167684939505 chr11 135006516 11512591 0.08527433594390363 0.3069692359229021 chr12 133851895 11679992 0.08726056511938064 0.3085034463624932 chr13 115169878 9434713 0.08191997042837885 0.2996734283343987 chr14 107349540 7978256 0.07432035572765379 0.28657747716448845 chr15 102531392 6499608 0.06339139529091734 0.26420936106610865 chr16 90354753 4639369 0.05134615331193479 0.23591663696655998 chr17 81195210 4350659 0.053582705186672956 0.24203569418329493 chr18 78077248 6830081 0.08747850590225721 0.30771054091431915 chr19 59128983 2123827 0.0359185443794966 0.19626100451602682 chr20 63025520 4022146 0.06381773605358591 0.26392853539991135 chr21 48129895 3101545 0.06444113372780057 0.2687816466383672 chr22 51304566 1417870 0.027636331627871095 0.1726813553939968 chrMT 16571 50 0.003017319413433106 0.05484719862481972 chrX 155270560 13228154 0.08519421840173694 0.3046239638720942 chrY 59373566 266410 0.004487013631621857 0.07140779543882658