BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153376.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 36,448,700 number of mapped reads = 36,179,560 (99.26%) number of supplementary alignments = 278,792 (0.76%) number of secondary alignments = 0 number of mapped bases = 3,506,825,851 bp number of sequenced bases = 3,506,198,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,934,903 duplication rate = 29.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2607 >>>>>>> ACTG content number of A's = 929,823,328 bp (26.52%) number of C's = 818,818,331 bp (23.35%) number of T's = 949,094,756 bp (27.07%) number of G's = 807,050,592 bp (23.02%) number of N's = 1,411,897 bp (0.04%) GC percentage = 46.37% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 9,411,948 number of insertions = 373,636 mapped reads with insertion percentage = 1.02% number of deletions = 296,376 mapped reads with deletion percentage = 0.81% homopolymer indels = 49.85% >>>>>>> Coverage mean coverageData = 1.1328X std coverageData = 10.8396X There is a 19.23% of reference with a coverageData >= 1X There is a 9.48% of reference with a coverageData >= 2X There is a 5.08% of reference with a coverageData >= 3X There is a 3.73% of reference with a coverageData >= 4X There is a 2.97% of reference with a coverageData >= 5X There is a 2.57% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 2.11% of reference with a coverageData >= 8X There is a 1.95% of reference with a coverageData >= 9X There is a 1.82% of reference with a coverageData >= 10X There is a 1.71% of reference with a coverageData >= 11X There is a 1.61% of reference with a coverageData >= 12X There is a 1.52% of reference with a coverageData >= 13X There is a 1.45% of reference with a coverageData >= 14X There is a 1.38% of reference with a coverageData >= 15X There is a 1.31% of reference with a coverageData >= 16X There is a 1.25% of reference with a coverageData >= 17X There is a 1.2% of reference with a coverageData >= 18X There is a 1.15% of reference with a coverageData >= 19X There is a 1.1% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 1.02% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.94% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.88% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.79% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.74% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.7% of reference with a coverageData >= 33X There is a 0.67% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.62% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.57% of reference with a coverageData >= 40X There is a 0.55% of reference with a coverageData >= 41X There is a 0.54% of reference with a coverageData >= 42X There is a 0.52% of reference with a coverageData >= 43X There is a 0.51% of reference with a coverageData >= 44X There is a 0.5% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.46% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 386647000 1.5512378603060732 15.465906857319505 chr2 243199373 253373566 1.0418347830197736 8.488718914556951 chr3 198022430 205574311 1.0381364929215342 8.117092436328173 chr4 191154276 113272686 0.5925720751336998 5.3065225368439926 chr5 180915260 219802314 1.2149462350494922 10.7063367198885 chr6 171115067 101854527 0.5952399679684548 5.946648184372547 chr7 159138663 161148171 1.0126274028078268 9.0813810139917 chr8 146364022 248980465 1.7011042850407596 21.656902305831057 chr9 141213431 73157534 0.518063568613385 5.04681765147197 chr10 135534747 185749125 1.3704908085304501 10.473195691813379 chr11 135006516 214174704 1.586402718517675 11.56619870344295 chr12 133851895 187397718 1.400037840330912 9.863158052245769 chr13 115169878 37311342 0.32396788681151506 3.3050968388496673 chr14 107349540 103800419 0.966938647338405 7.94510092032096 chr15 102531392 141212215 1.3772583424986564 10.62758941583244 chr16 90354753 152290464 1.6854726391648704 12.987016807241437 chr17 81195210 122155078 1.504461630187298 9.547073965799079 chr18 78077248 35010853 0.4484129999049147 4.233860522522789 chr19 59128983 147297372 2.491119659541582 17.30952572569739 chr20 63025520 72104364 1.1440502831234078 8.676550863929885 chr21 48129895 26987763 0.5607276517017126 5.106854105884016 chr22 51304566 50614690 0.9865533215893494 10.139408624263373 chrMT 16571 5884 0.3550781485728079 0.8149203129116177 chrX 155270560 264424280 1.7029904445504673 15.34601446863049 chrY 59373566 2479006 0.041752688393349995 1.493656560039651