BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083617.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 = 2,109,897 number of mapped reads = 1,883,622 (89.28%) number of supplementary alignments = 17,069 (0.81%) number of secondary alignments = 0 number of mapped bases = 123,974,561 bp number of sequenced bases = 123,928,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,484 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.794 >>>>>>> ACTG content number of A's = 32,839,791 bp (26.5%) number of C's = 23,051,039 bp (18.6%) number of T's = 38,998,987 bp (31.47%) number of G's = 29,033,539 bp (23.43%) number of N's = 5,581 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 901,249 number of insertions = 9,301 mapped reads with insertion percentage = 0.49% number of deletions = 28,018 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.4116X There is a 3.32% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 11014300 0.044189659210518074 0.7954227120180254 chr2 243199373 10851788 0.04462095385418613 0.5711987911797388 chr3 198022430 10354468 0.052289369441633454 0.27038632618716496 chr4 191154276 5769506 0.03018245848709134 0.21539671051791978 chr5 180915260 5891326 0.032564008143923295 0.21088679381608622 chr6 171115067 8532876 0.0498663042921872 0.35014628307719564 chr7 159138663 8924637 0.05608088463078265 0.6852936319826433 chr8 146364022 8420152 0.05752883724389591 0.3947252886384913 chr9 141213431 5002109 0.035422331746900196 0.3108343569011063 chr10 135534747 5634713 0.041573936755863794 0.31511634056808674 chr11 135006516 4706224 0.03485923597939525 0.32135131491270885 chr12 133851895 4361147 0.03258188462703498 0.21218350941514333 chr13 115169878 3696180 0.032093287447955796 0.20882897471917958 chr14 107349540 2699657 0.02514828661585322 0.1976898598451056 chr15 102531392 3145480 0.030678214141479712 0.2307065572631408 chr16 90354753 3633295 0.04021144299957303 0.2508663246860669 chr17 81195210 2734895 0.0336829598691844 0.23134101764070533 chr18 78077248 3255395 0.0416945407706993 0.6182047022551597 chr19 59128983 3770978 0.06377545847524554 0.5469146602652262 chr20 63025520 2769399 0.04394091472787531 0.25303984068636043 chr21 48129895 1951232 0.04054095692500472 0.24289324132786805 chr22 51304566 988279 0.019262983337584416 0.15982116037757935 chrMT 16571 38116 2.3001629352483253 2.171926478726374 chrX 155270560 5563970 0.035834030610825386 0.23955885823174564 chrY 59373566 264439 0.004453817040398079 0.10187594531150904