BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084794.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 = 1,324,050 number of mapped reads = 1,176,241 (88.84%) number of supplementary alignments = 13,321 (1.01%) number of secondary alignments = 0 number of mapped bases = 79,424,570 bp number of sequenced bases = 79,394,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,263 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8652 >>>>>>> ACTG content number of A's = 22,190,810 bp (27.95%) number of C's = 14,940,794 bp (18.82%) number of T's = 24,767,360 bp (31.2%) number of G's = 17,468,843 bp (22%) number of N's = 26,918 bp (0.03%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 638,594 number of insertions = 5,888 mapped reads with insertion percentage = 0.5% number of deletions = 18,180 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2194X There is a 2.22% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 5591024 0.02243133428341589 0.2863455435434536 chr2 243199373 7949469 0.0326870456199737 0.27310262778693806 chr3 198022430 5744946 0.029011592272653153 0.19139361596036114 chr4 191154276 5168845 0.027040174607446395 0.18891209777660253 chr5 180915260 4273085 0.023619262410478806 0.17331290456483162 chr6 171115067 4340674 0.02536698886954239 0.19160863578722173 chr7 159138663 4393846 0.02761017289682772 0.2210616749442075 chr8 146364022 3904361 0.026675688100454086 0.2653413647265624 chr9 141213431 3797117 0.02688920574417599 0.2256031887814131 chr10 135534747 3947212 0.02912324763479287 0.21956534154262233 chr11 135006516 3268051 0.024206616812480368 0.19893783786152477 chr12 133851895 3383193 0.02527564514495667 0.18084073698342457 chr13 115169878 2615500 0.022709931150573938 0.17044850973446943 chr14 107349540 2454297 0.022862668996998032 0.17943475931443392 chr15 102531392 2024125 0.01974151487185505 0.1593779314304484 chr16 90354753 2157925 0.023882805589651713 0.1847031374456877 chr17 81195210 2107062 0.025950570236840324 0.19745048756360917 chr18 78077248 2052890 0.02629306299320386 0.38643084902929004 chr19 59128983 1135260 0.019199721395512587 0.22418345957290714 chr20 63025520 1882767 0.02987308950406121 0.2030516259978791 chr21 48129895 1139236 0.023670028783565805 0.17647131801238788 chr22 51304566 681120 0.013276011339809404 0.12839855258165642 chrMT 16571 2232 0.13469313861565385 0.40732572055946054 chrX 155270560 5201007 0.03349641425908427 0.2182982330453776 chrY 59373566 209326 0.003525575674535028 0.08178163909374224