BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708574.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 = 4,236,376 number of mapped reads = 3,493,503 (82.46%) number of supplementary alignments = 72 (0%) number of secondary alignments = 0 number of mapped bases = 174,214,505 bp number of sequenced bases = 174,198,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,717 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6118 >>>>>>> ACTG content number of A's = 54,026,322 bp (31.01%) number of C's = 33,052,284 bp (18.97%) number of T's = 53,752,560 bp (30.86%) number of G's = 33,358,898 bp (19.15%) number of N's = 8,404 bp (0%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 276,254 number of insertions = 11,604 mapped reads with insertion percentage = 0.33% number of deletions = 9,361 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.2444X There is a 5.32% of reference with a coverageData >= 1X There is a 0.29% 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 12754148 0.05116997481823726 0.23382590790185476 chr2 243199373 14270237 0.058677112625615195 0.2487625369897731 chr3 198022430 12641761 0.06384004579683221 0.2589438892547033 chr4 191154276 13716138 0.07175428291230064 0.27461343778089714 chr5 180915260 12637449 0.06985286371088874 0.27149413370253145 chr6 171115067 11091885 0.06482120595493791 0.2615716245602251 chr7 159138663 9453066 0.05940144162201488 0.2509717789410243 chr8 146364022 10101174 0.06901405046111674 0.26988626023243895 chr9 141213431 7197748 0.05097070405434735 0.2330621069821236 chr10 135534747 7014882 0.051757074516101766 0.23310600538395782 chr11 135006516 7867611 0.05827578722200342 0.2486507176649462 chr12 133851895 7983792 0.05964646223350069 0.25168916057094654 chr13 115169878 7097375 0.06162527149677106 0.25603192756241017 chr14 107349540 5821218 0.05422676240624785 0.24041821722489892 chr15 102531392 4744546 0.04627408160029662 0.2220795303150061 chr16 90354753 3234586 0.03579873656452805 0.19451570814341493 chr17 81195210 2944341 0.03626249627287127 0.19558632397050305 chr18 78077248 4784780 0.061282641519332236 0.2537498751537811 chr19 59128983 1462299 0.024730663809996528 0.1611789728728724 chr20 63025520 2697937 0.04280705657010049 0.21299860962538564 chr21 48129895 2118611 0.04401860839297488 0.21813050772371906 chr22 51304566 988262 0.01926265198306131 0.14209445863910727 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 11320669 0.07290930746949068 0.2780241189558042 chrY 59373566 269790 0.004543941322304946 0.07018252822914298