BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124973.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,115,768 number of mapped reads = 2,933,348 (94.15%) number of supplementary alignments = 9,182 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,498,424 number of mapped paired reads (second in pair) = 1,434,924 number of mapped paired reads (both in pair) = 2,843,180 number of mapped paired reads (singletons) = 90,168 number of mapped bases = 178,845,716 bp number of sequenced bases = 178,731,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 308,856 duplication rate = 7.06% >>>>>>> Insert size mean insert size = 60,871.4498 std insert size = 2,250,777.3407 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 51.7283 >>>>>>> ACTG content number of A's = 49,496,520 bp (27.69%) number of C's = 31,710,746 bp (17.74%) number of T's = 53,332,264 bp (29.84%) number of G's = 44,191,762 bp (24.73%) number of N's = 0 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,589,738 number of insertions = 27,136 mapped reads with insertion percentage = 0.91% number of deletions = 68,468 mapped reads with deletion percentage = 2.3% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.7951X There is a 4.2% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 16899235 0.06780017210067453 0.3961603689691584 chr2 243199373 14924361 0.061366774165162015 1.0108700519106342 chr3 198022430 12974893 0.06552234007026375 0.3491274211462073 chr4 191154276 9513675 0.04976961645367536 1.1223778164058462 chr5 180915260 9311856 0.05147081567359216 0.2918958081627153 chr6 171115067 8986750 0.0525187533602754 0.3289733917930326 chr7 159138663 12434726 0.07813768047052148 0.4949491082909358 chr8 146364022 10136329 0.06925423926926523 0.35502605557691225 chr9 141213431 6588746 0.04665806894813001 0.3950231267731447 chr10 135534747 9585291 0.07072201935050648 2.3843022830386245 chr11 135006516 6766592 0.05012048455498252 0.3093156314263792 chr12 133851895 8337953 0.062292379200159995 0.3149572246484896 chr13 115169878 3839771 0.0333400631022636 0.22524336599864594 chr14 107349540 5556769 0.05176332381116864 0.3019120549055801 chr15 102531392 5049348 0.049246849199121374 0.27993272311824224 chr16 90354753 7129578 0.07890650755251359 1.3541428466806489 chr17 81195210 4240085 0.05222087608370001 0.37674041540389946 chr18 78077248 2663164 0.03410934770651752 0.4388951029717182 chr19 59128983 3497732 0.05915427295612374 0.36437956832964763 chr20 63025520 4429959 0.07028833716881669 0.46276097915365905 chr21 48129895 1861548 0.03867758282040715 0.5581318090700563 chr22 51304566 1629855 0.03176822507376829 0.24449357608881253 chrMT 16571 7651 0.4617102166435339 0.7281663351380393 chrX 155270560 7787344 0.05015338387392948 0.301778602195552 chrY 59373566 4692505 0.07903357194344703 1.9432916733868921