BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153316.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 = 142,741,762 number of mapped reads = 139,098,449 (97.45%) number of supplementary alignments = 863,059 (0.6%) number of secondary alignments = 0 number of mapped bases = 13,599,395,028 bp number of sequenced bases = 13,597,115,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,624,479 duplication rate = 32.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3628 >>>>>>> ACTG content number of A's = 3,441,639,592 bp (25.31%) number of C's = 3,357,579,446 bp (24.69%) number of T's = 3,472,627,396 bp (25.54%) number of G's = 3,323,060,177 bp (24.44%) number of N's = 2,208,406 bp (0.02%) GC percentage = 49.13% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 53,087,149 number of insertions = 789,552 mapped reads with insertion percentage = 0.56% number of deletions = 1,021,679 mapped reads with deletion percentage = 0.72% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 4.393X std coverageData = 33.6217X There is a 54.06% of reference with a coverageData >= 1X There is a 35.87% of reference with a coverageData >= 2X There is a 23.82% of reference with a coverageData >= 3X There is a 16.96% of reference with a coverageData >= 4X There is a 12.67% of reference with a coverageData >= 5X There is a 9.99% of reference with a coverageData >= 6X There is a 8.23% of reference with a coverageData >= 7X There is a 7.02% of reference with a coverageData >= 8X There is a 6.17% of reference with a coverageData >= 9X There is a 5.53% of reference with a coverageData >= 10X There is a 5.05% of reference with a coverageData >= 11X There is a 4.67% of reference with a coverageData >= 12X There is a 4.36% of reference with a coverageData >= 13X There is a 4.1% of reference with a coverageData >= 14X There is a 3.89% of reference with a coverageData >= 15X There is a 3.7% of reference with a coverageData >= 16X There is a 3.53% of reference with a coverageData >= 17X There is a 3.39% of reference with a coverageData >= 18X There is a 3.26% of reference with a coverageData >= 19X There is a 3.14% of reference with a coverageData >= 20X There is a 3.03% of reference with a coverageData >= 21X There is a 2.93% of reference with a coverageData >= 22X There is a 2.83% of reference with a coverageData >= 23X There is a 2.75% of reference with a coverageData >= 24X There is a 2.67% of reference with a coverageData >= 25X There is a 2.59% of reference with a coverageData >= 26X There is a 2.52% of reference with a coverageData >= 27X There is a 2.45% of reference with a coverageData >= 28X There is a 2.39% of reference with a coverageData >= 29X There is a 2.33% of reference with a coverageData >= 30X There is a 2.27% of reference with a coverageData >= 31X There is a 2.21% of reference with a coverageData >= 32X There is a 2.16% of reference with a coverageData >= 33X There is a 2.11% of reference with a coverageData >= 34X There is a 2.06% of reference with a coverageData >= 35X There is a 2.02% of reference with a coverageData >= 36X There is a 1.97% of reference with a coverageData >= 37X There is a 1.93% of reference with a coverageData >= 38X There is a 1.89% of reference with a coverageData >= 39X There is a 1.85% of reference with a coverageData >= 40X There is a 1.81% of reference with a coverageData >= 41X There is a 1.77% of reference with a coverageData >= 42X There is a 1.74% of reference with a coverageData >= 43X There is a 1.7% of reference with a coverageData >= 44X There is a 1.67% of reference with a coverageData >= 45X There is a 1.64% of reference with a coverageData >= 46X There is a 1.61% of reference with a coverageData >= 47X There is a 1.58% of reference with a coverageData >= 48X There is a 1.55% of reference with a coverageData >= 49X There is a 1.52% of reference with a coverageData >= 50X There is a 1.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1256081053 5.039429984007944 31.98659273352919 chr2 243199373 789756266 3.247361439537922 19.11705517376939 chr3 198022430 646839666 3.266496961985569 17.780923420758448 chr4 191154276 454694258 2.3786768860980123 22.559729259207913 chr5 180915260 798752489 4.415064207408485 54.08249194987046 chr6 171115067 393241870 2.298113643025953 13.754656046427652 chr7 159138663 666597636 4.188784946622305 47.707808992457025 chr8 146364022 820157831 5.603548056365929 65.02889179252138 chr9 141213431 307438715 2.1771209213095317 12.421060517941369 chr10 135534747 698389206 5.1528425105629925 26.708473359280273 chr11 135006516 650661063 4.819478957593424 22.675994871308152 chr12 133851895 567237125 4.237796745425233 20.698858761045862 chr13 115169878 117139412 1.0171011208330012 6.931304768551235 chr14 107349540 319708492 2.9782008567526232 15.88460367604487 chr15 102531392 727093628 7.091424526841497 40.154779497614996 chr16 90354753 785433187 8.692771115206302 53.61552925326537 chr17 81195210 749656015 9.232761575467322 46.63262661265874 chr18 78077248 162201220 2.077445403813413 12.116283464523047 chr19 59128983 942865682 15.945914070600537 61.10478132943608 chr20 63025520 459162197 7.28533770129941 35.187049231530324 chr21 48129895 178871266 3.7164275135027824 32.32426327767002 chr22 51304566 292761497 5.7063438953951975 30.65184248196027 chrMT 16571 63928 3.857823909239032 2.570591557909916 chrX 155270560 795785800 5.125155728168946 29.318687228579083 chrY 59373566 18805526 0.3167322980061531 14.318493516033962