BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082704.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 = 3,350,825 number of mapped reads = 3,106,246 (92.7%) number of supplementary alignments = 14,157 (0.42%) number of secondary alignments = 0 number of mapped bases = 205,968,812 bp number of sequenced bases = 205,890,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,367 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.441 >>>>>>> ACTG content number of A's = 56,604,247 bp (27.49%) number of C's = 35,444,531 bp (17.22%) number of T's = 68,498,691 bp (33.27%) number of G's = 45,286,943 bp (22%) number of N's = 56,150 bp (0.03%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,881,406 number of insertions = 18,618 mapped reads with insertion percentage = 0.59% number of deletions = 49,169 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 0.5324X There is a 5.47% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20330611 0.08156694221435862 0.8624661740681192 chr2 243199373 19292917 0.07932963297565739 0.71923632702295 chr3 198022430 18333946 0.09258519855553737 0.35941543139497345 chr4 191154276 11157532 0.058369251441699375 0.291069629103351 chr5 180915260 13293450 0.0734788762429438 0.32128426676048294 chr6 171115067 13301049 0.07773160618287342 0.5069165305918338 chr7 159138663 8905333 0.05595958161342602 0.7644222031065585 chr8 146364022 14950731 0.10214758241612136 0.5184423598606086 chr9 141213431 6929177 0.049068824055411554 0.55967827575698 chr10 135534747 8833650 0.06517627542404311 0.4617813529889065 chr11 135006516 8699718 0.06443924528798299 0.47873529308252283 chr12 133851895 7258809 0.0542301549036717 0.2777441381118032 chr13 115169878 4957590 0.04304589087087511 0.2374341456411894 chr14 107349540 4659828 0.04340799224663655 0.2846499041011911 chr15 102531392 3942449 0.03845114089546351 0.22520341069171063 chr16 90354753 6832670 0.07562048230047179 0.3614270042621269 chr17 81195210 5309487 0.06539162839778356 0.40234102682135087 chr18 78077248 5322683 0.06817201087825227 1.190061013336242 chr19 59128983 2861388 0.048392308726162264 0.5889196558196022 chr20 63025520 4933104 0.07827153191278707 0.3522631607215 chr21 48129895 3783920 0.0786189124243882 0.34441953768666145 chr22 51304566 2627449 0.051212771198571296 0.2630388237494185 chrMT 16571 1611 0.09721803150081468 0.32899216554372396 chrX 155270560 9094042 0.05856900367977033 0.35717377171001363 chrY 59373566 355668 0.005990342570968366 0.11667188114216168