BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549082.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,875,802 number of mapped reads = 6,953,951 (88.3%) number of secondary alignments = 0 number of mapped bases = 276,370,734 bp number of sequenced bases = 276,346,140 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 236,865 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2565 >>>>>>> ACTG content number of A's = 82,236,328 bp (29.76%) number of C's = 55,632,448 bp (20.13%) number of T's = 83,659,900 bp (30.27%) number of G's = 54,750,643 bp (19.81%) number of N's = 66,821 bp (0.02%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,056,826 number of insertions = 6,176 mapped reads with insertion percentage = 0.09% number of deletions = 19,663 mapped reads with deletion percentage = 0.28% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0893X std coverageData = 0.6388X There is a 7.44% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 22302828 0.08947952831780508 1.4893944307690876 chr2 243199373 24375674 0.10022918110072594 0.5160940958776422 chr3 198022430 19884315 0.10041445809951934 0.3680715772891161 chr4 191154276 19254977 0.10073003546099069 0.37158503356819045 chr5 180915260 17972723 0.09934332239303639 0.37195558512399346 chr6 171115067 17070356 0.09975951445584859 0.4453779862220159 chr7 159138663 15522310 0.09753952752512443 0.7223042486084859 chr8 146364022 14707804 0.10048783709974846 0.5663051349035789 chr9 141213431 11830835 0.08377981411697305 0.5111482733984812 chr10 135534747 13182635 0.09726387728454608 0.5423885611520571 chr11 135006516 12837322 0.09508668455676614 0.543376078441234 chr12 133851895 12779378 0.09547401626252658 0.3742380954110778 chr13 115169878 9517426 0.08263815300733408 0.3263912801483331 chr14 107349540 8668860 0.08075358310804126 0.3810136711704668 chr15 102531392 7866196 0.07671987911760722 0.3164258141705025 chr16 90354753 7178625 0.07944933455797284 0.3749054478452665 chr17 81195210 6387953 0.0786740129128307 0.3733533886447505 chr18 78077248 7687563 0.09846098827663598 1.0721626443358356 chr19 59128983 4280501 0.0723926031333906 1.1191544306722603 chr20 63025520 5469907 0.08678876429738303 0.34859288760387075 chr21 48129895 3609657 0.07499823134872827 0.3686319708695923 chr22 51304566 2551678 0.049735885106210624 0.28987128192352407 chrMT 16571 10220 0.6167400881057269 1.0607324630885597 chrX 155270560 9374333 0.06037418168647038 0.3461277454962877 chrY 59373566 2046658 0.03447086199942918 0.2693274010136978