BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618662.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 28,840,088 number of mapped reads = 27,231,165 (94.42%) number of supplementary alignments = 72,756 (0.25%) number of secondary alignments = 0 number of mapped bases = 2,657,921,509 bp number of sequenced bases = 2,656,099,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,585,631 duplication rate = 18.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3625 >>>>>>> ACTG content number of A's = 726,923,244 bp (27.37%) number of C's = 580,279,865 bp (21.85%) number of T's = 740,930,735 bp (27.9%) number of G's = 581,553,783 bp (21.9%) number of N's = 26,411,436 bp (0.99%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0197 number of mismatches = 51,588,127 number of insertions = 486,069 mapped reads with insertion percentage = 1.76% number of deletions = 1,319,656 mapped reads with deletion percentage = 4.73% homopolymer indels = 53.29% >>>>>>> Coverage mean coverageData = 0.8586X std coverageData = 3.3592X There is a 22.73% of reference with a coverageData >= 1X There is a 14.02% of reference with a coverageData >= 2X There is a 9.61% of reference with a coverageData >= 3X There is a 6.98% of reference with a coverageData >= 4X There is a 5.28% of reference with a coverageData >= 5X There is a 4.11% of reference with a coverageData >= 6X There is a 3.28% of reference with a coverageData >= 7X There is a 2.66% of reference with a coverageData >= 8X There is a 2.19% of reference with a coverageData >= 9X There is a 1.82% of reference with a coverageData >= 10X There is a 1.53% of reference with a coverageData >= 11X There is a 1.3% of reference with a coverageData >= 12X There is a 1.11% of reference with a coverageData >= 13X There is a 0.96% of reference with a coverageData >= 14X There is a 0.83% of reference with a coverageData >= 15X There is a 0.72% of reference with a coverageData >= 16X There is a 0.63% of reference with a coverageData >= 17X There is a 0.55% of reference with a coverageData >= 18X There is a 0.49% of reference with a coverageData >= 19X There is a 0.43% of reference with a coverageData >= 20X There is a 0.39% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 231596027 0.9291693078670403 3.8685954375957166 chr2 243199373 222982897 0.9168728284509188 3.9622977461584026 chr3 198022430 172119974 0.8691943331874071 2.8130766347783718 chr4 191154276 131857343 0.6897954142548189 2.875296677200524 chr5 180915260 150760363 0.8333203235592177 2.720798829206602 chr6 171115067 143291813 0.8374003266468639 2.8658719822845615 chr7 159138663 133705458 0.8401821121244433 2.8599070389318504 chr8 146364022 128487802 0.8778646572038038 2.8956220859347344 chr9 141213431 116241015 0.8231583509928315 3.054283328417063 chr10 135534747 133444114 0.9845749297041887 3.192354878037818 chr11 135006516 132711648 0.9830017982243168 3.4050505776040962 chr12 133851895 116727800 0.8720668467189052 2.9868769436683564 chr13 115169878 71487968 0.6207175803381506 2.369938183539755 chr14 107349540 82997445 0.7731513800618056 2.7864892553037754 chr15 102531392 88524129 0.8633856155976113 3.0400460121133905 chr16 90354753 94035694 1.040738764456586 6.831734604257422 chr17 81195210 84365600 1.0390465151823611 3.503043355893523 chr18 78077248 68296315 0.8747274878335876 3.280563445643055 chr19 59128983 56003424 0.9471399837876461 3.616061047548639 chr20 63025520 74206374 1.177402011121844 3.6451570581815247 chr21 48129895 34716959 0.7213179875002844 4.97525137637499 chr22 51304566 46439015 0.9051633922797436 3.5163108930668554 chrMT 16571 1853 0.1118218574618309 0.6928611616572694 chrX 155270560 138628379 0.8928181813732108 2.889982880093785 chrY 59373566 4292100 0.07228974591150547 1.927152107786652