BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080696.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,045,546 number of mapped reads = 1,644,107 (80.37%) number of supplementary alignments = 15,388 (0.75%) number of secondary alignments = 0 number of mapped bases = 111,576,069 bp number of sequenced bases = 111,534,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,934 duplication rate = 5.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1417 >>>>>>> ACTG content number of A's = 31,912,669 bp (28.61%) number of C's = 20,275,036 bp (18.18%) number of T's = 35,822,732 bp (32.12%) number of G's = 23,522,038 bp (21.09%) number of N's = 1,655 bp (0%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 884,110 number of insertions = 8,832 mapped reads with insertion percentage = 0.53% number of deletions = 23,805 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3561X There is a 2.83% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 8980533 0.036030132899849424 0.49105060675159545 chr2 243199373 9842656 0.040471551709140303 0.3520198338930998 chr3 198022430 7368573 0.037210799806870365 0.23546435626168719 chr4 191154276 7901950 0.04133807605747726 0.25902373453626515 chr5 180915260 6905179 0.03816802960678939 0.23919844306509602 chr6 171115067 6605808 0.0386044789381405 0.2656706919693765 chr7 159138663 6158579 0.03869945168510056 0.48200469163932147 chr8 146364022 6045779 0.04130645576274202 0.8799356108978513 chr9 141213431 4597936 0.03256018898089092 0.27309839189290264 chr10 135534747 5082761 0.03750153456958163 0.2866402156200731 chr11 135006516 5078018 0.03761313268761043 0.2849434664825458 chr12 133851895 5001458 0.037365612193985 0.23841832566945437 chr13 115169878 3631794 0.031534235019333785 0.2197612971108691 chr14 107349540 3378713 0.03147394017710742 0.22887246793596294 chr15 102531392 3040521 0.029654537412307832 0.20973128473128924 chr16 90354753 2798271 0.03096982623592585 0.22542613648798465 chr17 81195210 2615111 0.032207700429618936 0.23439321016293005 chr18 78077248 3056062 0.03914151789776197 0.4322854239423689 chr19 59128983 1743799 0.029491442462320043 0.32238673169301213 chr20 63025520 2131347 0.033817206109525155 0.23074081275973898 chr21 48129895 1493346 0.03102741030288971 0.22643615389257582 chr22 51304566 1052075 0.02050645940558195 0.171634907807583 chrMT 16571 61665 3.7212600325870495 2.721051712879679 chrX 155270560 6716832 0.04325888951517918 0.26942130044421836 chrY 59373566 287303 0.004838904235598717 0.12870592713408252