BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090155.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 = 17,775,453 number of mapped reads = 15,642,926 (88%) number of supplementary alignments = 110,439 (0.62%) number of secondary alignments = 0 number of mapped bases = 1,006,980,287 bp number of sequenced bases = 1,006,603,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,957,509 duplication rate = 9.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2673 >>>>>>> ACTG content number of A's = 267,126,869 bp (26.54%) number of C's = 180,736,320 bp (17.96%) number of T's = 320,009,146 bp (31.79%) number of G's = 237,898,744 bp (23.63%) number of N's = 832,270 bp (0.08%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 8,704,732 number of insertions = 72,071 mapped reads with insertion percentage = 0.46% number of deletions = 221,304 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.3253X std coverageData = 2.11X There is a 18.06% of reference with a coverageData >= 1X There is a 7.18% of reference with a coverageData >= 2X There is a 3.17% of reference with a coverageData >= 3X There is a 1.53% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% 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% 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 92910198 0.37275814049024975 4.015563767356131 chr2 243199373 85979546 0.3535352288922225 2.573556240280445 chr3 198022430 94338211 0.4764016429855951 1.1868175577047642 chr4 191154276 48111029 0.25168690968754476 0.9422997986586726 chr5 180915260 45278203 0.2502729896858894 0.8234049744223649 chr6 171115067 56857923 0.3322788810876601 1.2295178127227275 chr7 159138663 75360301 0.4735511759326519 3.5161726737156425 chr8 146364022 88532183 0.6048766752255551 4.003449732688081 chr9 141213431 32056516 0.22700755709278106 1.5811220725683197 chr10 135534747 30497108 0.22501320639201106 1.5908503680267476 chr11 135006516 43288613 0.32064091632436464 1.5365278067242336 chr12 133851895 37431157 0.2796460744915117 0.9137856503680193 chr13 115169878 33222951 0.28846909953312616 0.8549938064087198 chr14 107349540 35771379 0.33322340272720313 1.0539466423950485 chr15 102531392 27514410 0.26835108217393555 0.8895990909476629 chr16 90354753 21689402 0.24004716165844645 0.8811556895883331 chr17 81195210 21229644 0.2614642415482391 1.0628636104969156 chr18 78077248 37738088 0.4833429579895029 2.9258042948000305 chr19 59128983 17394810 0.2941841566935119 2.1706775973893824 chr20 63025520 25100724 0.39826286240875125 1.1149746507679659 chr21 48129895 15084191 0.31340585721203007 1.0473335505707955 chr22 51304566 8565748 0.16695878491594685 0.6324967926770512 chrMT 16571 1048614 63.28006758795486 33.16170145336406 chrX 155270560 29802259 0.191937602337494 0.956546778445315 chrY 59373566 2177079 0.036667479261730716 1.1149250326894922