BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163150.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 = 51,037,010 number of mapped reads = 50,480,279 (98.91%) number of supplementary alignments = 266,300 (0.52%) number of secondary alignments = 0 number of mapped bases = 4,957,058,300 bp number of sequenced bases = 4,956,474,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,376,966 duplication rate = 37.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0231 >>>>>>> ACTG content number of A's = 1,202,396,574 bp (24.26%) number of C's = 1,276,163,930 bp (25.75%) number of T's = 1,202,947,146 bp (24.27%) number of G's = 1,274,806,383 bp (25.72%) number of N's = 160,789 bp (0%) GC percentage = 51.47% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 15,180,703 number of insertions = 359,316 mapped reads with insertion percentage = 0.7% number of deletions = 243,834 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 1.6013X std coverageData = 20.461X There is a 7.83% of reference with a coverageData >= 1X There is a 5.25% of reference with a coverageData >= 2X There is a 4.07% of reference with a coverageData >= 3X There is a 3.62% of reference with a coverageData >= 4X There is a 3.28% of reference with a coverageData >= 5X There is a 3.04% of reference with a coverageData >= 6X There is a 2.84% of reference with a coverageData >= 7X There is a 2.68% of reference with a coverageData >= 8X There is a 2.53% of reference with a coverageData >= 9X There is a 2.41% of reference with a coverageData >= 10X There is a 2.3% of reference with a coverageData >= 11X There is a 2.2% of reference with a coverageData >= 12X There is a 2.1% of reference with a coverageData >= 13X There is a 2.02% of reference with a coverageData >= 14X There is a 1.94% of reference with a coverageData >= 15X There is a 1.87% of reference with a coverageData >= 16X There is a 1.8% of reference with a coverageData >= 17X There is a 1.74% of reference with a coverageData >= 18X There is a 1.68% of reference with a coverageData >= 19X There is a 1.63% of reference with a coverageData >= 20X There is a 1.58% of reference with a coverageData >= 21X There is a 1.53% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.44% of reference with a coverageData >= 24X There is a 1.4% of reference with a coverageData >= 25X There is a 1.36% of reference with a coverageData >= 26X There is a 1.32% of reference with a coverageData >= 27X There is a 1.28% of reference with a coverageData >= 28X There is a 1.25% of reference with a coverageData >= 29X There is a 1.22% of reference with a coverageData >= 30X There is a 1.19% of reference with a coverageData >= 31X There is a 1.16% of reference with a coverageData >= 32X There is a 1.13% of reference with a coverageData >= 33X There is a 1.1% of reference with a coverageData >= 34X There is a 1.07% of reference with a coverageData >= 35X There is a 1.05% of reference with a coverageData >= 36X There is a 1.02% of reference with a coverageData >= 37X There is a 1% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.96% of reference with a coverageData >= 40X There is a 0.93% of reference with a coverageData >= 41X There is a 0.91% of reference with a coverageData >= 42X There is a 0.89% of reference with a coverageData >= 43X There is a 0.88% of reference with a coverageData >= 44X There is a 0.86% of reference with a coverageData >= 45X There is a 0.84% of reference with a coverageData >= 46X There is a 0.82% of reference with a coverageData >= 47X There is a 0.81% of reference with a coverageData >= 48X There is a 0.79% of reference with a coverageData >= 49X There is a 0.77% of reference with a coverageData >= 50X There is a 0.76% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 535333761 2.147773028015846 20.76233934248754 chr2 243199373 304857219 1.2535279809294575 14.704923501835914 chr3 198022430 250709979 1.2660685913206904 14.38360002672847 chr4 191154276 168812855 0.8831236137244453 13.784403728006875 chr5 180915260 255157306 1.4103691750491363 19.98277637408703 chr6 171115067 246965321 1.4432704572999409 17.629582171003534 chr7 159138663 263996149 1.658906415469885 20.38266319021448 chr8 146364022 243973435 1.6668948534360446 40.40666711354916 chr9 141213431 233858714 1.6560656613463347 19.339799593060853 chr10 135534747 208011274 1.534744990522615 24.437381571796298 chr11 135006516 235162407 1.7418596817949143 16.6019372513133 chr12 133851895 233344473 1.7433034698537515 19.61641580752594 chr13 115169878 91087609 0.790897850912024 10.457863076171886 chr14 107349540 124060640 1.1556699730618314 13.750662260088102 chr15 102531392 227389149 2.2177515058022426 20.881259862964537 chr16 90354753 182640786 2.021374415134531 18.100318114351893 chr17 81195210 247050682 3.042675571625469 24.552044404660624 chr18 78077248 82716530 1.0594191280922196 14.013303731375558 chr19 59128983 290574068 4.914240923101958 37.051523437616055 chr20 63025520 108384440 1.7196913250378576 19.761510951944818 chr21 48129895 65903951 1.369293471344577 30.07144822127164 chr22 51304566 93123802 1.815117235374333 16.2692681051253 chrMT 16571 753 0.04544083036630258 0.23953355376701005 chrX 155270560 259101764 1.6687114672607608 21.02376843895222 chrY 59373566 4841233 0.08153852507359925 4.741492125380189