BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618612.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 = 45,902,432 number of mapped reads = 42,965,428 (93.6%) number of supplementary alignments = 289,000 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,975,555 number of mapped paired reads (second in pair) = 20,989,873 number of mapped paired reads (both in pair) = 41,229,356 number of mapped paired reads (singletons) = 1,736,072 number of mapped bases = 4,010,822,079 bp number of sequenced bases = 4,007,993,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,025,817 duplication rate = 29.22% >>>>>>> Insert size mean insert size = 150,371.3233 std insert size = 3,884,857.4593 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 51.8831 >>>>>>> ACTG content number of A's = 1,085,757,010 bp (27.09%) number of C's = 878,625,340 bp (21.92%) number of T's = 1,106,462,047 bp (27.61%) number of G's = 935,324,772 bp (23.34%) number of N's = 1,824,506 bp (0.05%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 54,065,850 number of insertions = 760,989 mapped reads with insertion percentage = 1.74% number of deletions = 2,060,491 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.35% >>>>>>> Coverage mean coverageData = 1.2956X std coverageData = 5.5399X There is a 24.35% of reference with a coverageData >= 1X There is a 16.84% of reference with a coverageData >= 2X There is a 12.68% of reference with a coverageData >= 3X There is a 10.06% of reference with a coverageData >= 4X There is a 8.16% of reference with a coverageData >= 5X There is a 6.76% of reference with a coverageData >= 6X There is a 5.67% of reference with a coverageData >= 7X There is a 4.81% of reference with a coverageData >= 8X There is a 4.12% of reference with a coverageData >= 9X There is a 3.55% of reference with a coverageData >= 10X There is a 3.09% of reference with a coverageData >= 11X There is a 2.7% of reference with a coverageData >= 12X There is a 2.37% of reference with a coverageData >= 13X There is a 2.09% of reference with a coverageData >= 14X There is a 1.85% of reference with a coverageData >= 15X There is a 1.65% of reference with a coverageData >= 16X There is a 1.47% of reference with a coverageData >= 17X There is a 1.32% of reference with a coverageData >= 18X There is a 1.18% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 0.96% of reference with a coverageData >= 21X There is a 0.87% of reference with a coverageData >= 22X There is a 0.79% of reference with a coverageData >= 23X There is a 0.72% of reference with a coverageData >= 24X There is a 0.65% of reference with a coverageData >= 25X There is a 0.6% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.5% of reference with a coverageData >= 28X There is a 0.46% of reference with a coverageData >= 29X There is a 0.42% of reference with a coverageData >= 30X There is a 0.39% of reference with a coverageData >= 31X There is a 0.36% of reference with a coverageData >= 32X There is a 0.33% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 367100202 1.4728155963150038 7.302735162321398 chr2 243199373 346819862 1.4260721881055178 6.3291468497484855 chr3 198022430 266413638 1.3453710168085504 5.16176380189588 chr4 191154276 212011063 1.1091097067585347 4.537369601499025 chr5 180915260 239606428 1.3244124790799847 4.664363316289951 chr6 171115067 229172050 1.3392862125928398 4.640003783123002 chr7 159138663 210615425 1.323471122790569 5.106052377095816 chr8 146364022 205404491 1.4033810235140982 4.882889119292555 chr9 141213431 183594155 1.3001182231738282 6.343527247192792 chr10 135534747 208173922 1.5359450370317214 5.049586860414912 chr11 135006516 211145409 1.5639645793096386 5.915090125320713 chr12 133851895 188565576 1.4087628419455698 5.107331202450343 chr13 115169878 110593336 0.9602626825739974 3.646775449095267 chr14 107349540 128671404 1.198620916307606 4.673799816655949 chr15 102531392 135108990 1.317732914422931 4.915490334885299 chr16 90354753 144284159 1.5968629674633719 9.07122095390516 chr17 81195210 135625566 1.670364126159659 5.701313548809212 chr18 78077248 108536892 1.390121895689766 6.555709754450576 chr19 59128983 93966136 1.589172200035979 7.097427792871375 chr20 63025520 116327791 1.8457252078205781 5.661502207398575 chr21 48129895 51097335 1.061654819733141 6.682283304002445 chr22 51304566 72652595 1.4161038805006168 5.639703291911077 chrMT 16571 10999 0.6637499245670146 3.011421012263661 chrX 155270560 8977048 0.05781551892387069 1.3645847274047058 chrY 59373566 36347607 0.6121850083924554 3.9564344937573366