BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089702.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 26,790,716 number of mapped reads = 22,155,787 (82.7%) number of supplementary alignments = 873 (0%) number of secondary alignments = 0 number of mapped bases = 1,032,660,324 bp number of sequenced bases = 1,032,447,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,486,859 duplication rate = 8.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5675 >>>>>>> ACTG content number of A's = 328,418,524 bp (31.81%) number of C's = 209,400,557 bp (20.28%) number of T's = 268,964,987 bp (26.05%) number of G's = 225,629,724 bp (21.85%) number of N's = 33,364 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 5,536,703 number of insertions = 47,865 mapped reads with insertion percentage = 0.22% number of deletions = 143,562 mapped reads with deletion percentage = 0.65% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.3336X std coverageData = 1.7449X There is a 17.05% of reference with a coverageData >= 1X There is a 6.93% of reference with a coverageData >= 2X There is a 3.37% of reference with a coverageData >= 3X There is a 1.85% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.7% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 88990080 0.35703052471030755 2.0624367833667048 chr2 243199373 83656795 0.34398441890719844 2.7194308000884293 chr3 198022430 87298389 0.44085101369577173 1.368680179558382 chr4 191154276 38897292 0.2034863818583896 0.8654581681698647 chr5 180915260 46984827 0.2597062680063583 0.9275767775520947 chr6 171115067 69345525 0.4052566861338984 1.5193646335760638 chr7 159138663 59298798 0.3726234522907862 2.277219716799599 chr8 146364022 81360104 0.5558750223466803 3.29883479808386 chr9 141213431 37313889 0.2642375355924891 1.6417723078535549 chr10 135534747 46481970 0.3429524238533459 1.5940775645396483 chr11 135006516 52377518 0.38796288913936566 1.6708861986710248 chr12 133851895 37607980 0.2809671092067841 1.0134985400418426 chr13 115169878 31880407 0.27681202371335323 0.9615820774234415 chr14 107349540 37209049 0.34661582154893256 1.2363228914954294 chr15 102531392 28014513 0.27322864201434033 0.9501563944671799 chr16 90354753 21668054 0.23981089295877994 1.0028284140230967 chr17 81195210 26174475 0.32236476757680654 1.190425769339205 chr18 78077248 53903324 0.6903845278972948 2.510856755283906 chr19 59128983 18464021 0.3122668455163519 2.0467471622325837 chr20 63025520 24035626 0.3813633905757541 1.2302014012170912 chr21 48129895 17530289 0.3642286981926721 1.3294657351661048 chr22 51304566 8929357 0.1740460488448533 0.7398722361842341 chrMT 16571 195124 11.775028664534428 11.050216753497546 chrX 155270560 32631704 0.21016027764696668 1.2923477491612432 chrY 59373566 2411214 0.04061090081737721 0.6600262121663025