BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153372.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 = 63,640,482 number of mapped reads = 62,882,077 (98.81%) number of supplementary alignments = 349,196 (0.55%) number of secondary alignments = 0 number of mapped bases = 6,257,902,859 bp number of sequenced bases = 6,257,056,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,654,721 duplication rate = 34.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8586 >>>>>>> ACTG content number of A's = 1,621,743,225 bp (25.92%) number of C's = 1,502,167,497 bp (24.01%) number of T's = 1,633,003,940 bp (26.1%) number of G's = 1,499,852,250 bp (23.97%) number of N's = 289,340 bp (0%) GC percentage = 47.98% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 18,745,715 number of insertions = 547,502 mapped reads with insertion percentage = 0.86% number of deletions = 378,696 mapped reads with deletion percentage = 0.59% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 2.0215X std coverageData = 20.5531X There is a 10.42% of reference with a coverageData >= 1X There is a 6.6% of reference with a coverageData >= 2X There is a 5.41% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 4.45% of reference with a coverageData >= 5X There is a 4.15% of reference with a coverageData >= 6X There is a 3.9% of reference with a coverageData >= 7X There is a 3.69% of reference with a coverageData >= 8X There is a 3.5% of reference with a coverageData >= 9X There is a 3.34% of reference with a coverageData >= 10X There is a 3.19% of reference with a coverageData >= 11X There is a 3.05% of reference with a coverageData >= 12X There is a 2.93% of reference with a coverageData >= 13X There is a 2.81% of reference with a coverageData >= 14X There is a 2.7% of reference with a coverageData >= 15X There is a 2.6% of reference with a coverageData >= 16X There is a 2.51% of reference with a coverageData >= 17X There is a 2.42% of reference with a coverageData >= 18X There is a 2.34% of reference with a coverageData >= 19X There is a 2.26% of reference with a coverageData >= 20X There is a 2.19% of reference with a coverageData >= 21X There is a 2.12% of reference with a coverageData >= 22X There is a 2.05% of reference with a coverageData >= 23X There is a 1.99% of reference with a coverageData >= 24X There is a 1.93% of reference with a coverageData >= 25X There is a 1.87% of reference with a coverageData >= 26X There is a 1.82% of reference with a coverageData >= 27X There is a 1.77% of reference with a coverageData >= 28X There is a 1.72% of reference with a coverageData >= 29X There is a 1.67% of reference with a coverageData >= 30X There is a 1.62% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.54% of reference with a coverageData >= 33X There is a 1.5% of reference with a coverageData >= 34X There is a 1.46% of reference with a coverageData >= 35X There is a 1.42% of reference with a coverageData >= 36X There is a 1.39% of reference with a coverageData >= 37X There is a 1.35% of reference with a coverageData >= 38X There is a 1.32% of reference with a coverageData >= 39X There is a 1.29% of reference with a coverageData >= 40X There is a 1.26% of reference with a coverageData >= 41X There is a 1.23% of reference with a coverageData >= 42X There is a 1.2% of reference with a coverageData >= 43X There is a 1.17% of reference with a coverageData >= 44X There is a 1.15% of reference with a coverageData >= 45X There is a 1.12% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.07% of reference with a coverageData >= 48X There is a 1.05% of reference with a coverageData >= 49X There is a 1.02% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 643730117 2.5826620387838473 21.9749709306078 chr2 243199373 400195499 1.6455449455455626 13.84423270439891 chr3 198022430 302317868 1.526684972000394 12.663518494132752 chr4 191154276 233270684 1.2203267898647479 12.921374498907923 chr5 180915260 416491938 2.302138238642777 32.7840620285951 chr6 171115067 223301648 1.3049794615689803 11.323991667771141 chr7 159138663 297557310 1.869798981533482 19.06934896772681 chr8 146364022 367876035 2.513432126099951 41.93264650415734 chr9 141213431 205241231 1.4534115455349286 13.684789241028929 chr10 135534747 267994741 1.9773139134571889 16.037602373567328 chr11 135006516 275553692 2.0410399450645773 15.157862703499799 chr12 133851895 280128471 2.092824094869931 15.990641261016185 chr13 115169878 76269843 0.6622377684553942 7.075403747521509 chr14 107349540 151507232 1.411344957789293 12.125658761290326 chr15 102531392 333022688 3.2480070884046905 24.93312046963777 chr16 90354753 288020126 3.1876588274221724 24.64820401621533 chr17 81195210 264260836 3.2546357845493596 20.855376443151872 chr18 78077248 72374874 0.9269649719211415 8.919578560836891 chr19 59128983 405123099 6.851514747006557 36.55481078626898 chr20 63025520 147397434 2.3386944526598112 16.888474113148742 chr21 48129895 79041153 1.642246528898515 26.90317682049147 chr22 51304566 106068034 2.0674189895690764 16.401745121719916 chrMT 16571 835 0.05038923420433287 0.2874189954115475 chrX 155270560 414106140 2.6669971435666877 23.663848125717514 chrY 59373566 7051331 0.11876212724026042 5.3875010984898415