BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 101,159,220 number of mapped reads = 99,294,419 (98.16%) number of supplementary alignments = 2,569,975 (2.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 50,019,016 number of mapped paired reads (second in pair) = 49,275,403 number of mapped paired reads (both in pair) = 98,386,948 number of mapped paired reads (singletons) = 907,471 number of mapped bases = 13,046,801,195 bp number of sequenced bases = 13,036,065,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,622,960 duplication rate = 23.27% >>>>>>> Insert size mean insert size = 144,104.4361 std insert size = 3,577,833.3653 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 53.271 >>>>>>> ACTG content number of A's = 3,744,002,714 bp (28.72%) number of C's = 2,507,840,544 bp (19.24%) number of T's = 3,875,608,988 bp (29.73%) number of G's = 2,908,316,988 bp (22.31%) number of N's = 296,054 bp (0%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 156,450,359 number of insertions = 2,658,589 mapped reads with insertion percentage = 2.47% number of deletions = 4,823,021 mapped reads with deletion percentage = 4.63% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 4.2145X std coverageData = 62.1744X There is a 51.35% of reference with a coverageData >= 1X There is a 40.01% of reference with a coverageData >= 2X There is a 32.88% of reference with a coverageData >= 3X There is a 27.9% of reference with a coverageData >= 4X There is a 23.95% of reference with a coverageData >= 5X There is a 20.78% of reference with a coverageData >= 6X There is a 18.17% of reference with a coverageData >= 7X There is a 15.98% of reference with a coverageData >= 8X There is a 14.13% of reference with a coverageData >= 9X There is a 12.56% of reference with a coverageData >= 10X There is a 11.2% of reference with a coverageData >= 11X There is a 10.03% of reference with a coverageData >= 12X There is a 9.01% of reference with a coverageData >= 13X There is a 8.11% of reference with a coverageData >= 14X There is a 7.33% of reference with a coverageData >= 15X There is a 6.63% of reference with a coverageData >= 16X There is a 6.02% of reference with a coverageData >= 17X There is a 5.47% of reference with a coverageData >= 18X There is a 4.99% of reference with a coverageData >= 19X There is a 4.55% of reference with a coverageData >= 20X There is a 4.16% of reference with a coverageData >= 21X There is a 3.81% of reference with a coverageData >= 22X There is a 3.49% of reference with a coverageData >= 23X There is a 3.21% of reference with a coverageData >= 24X There is a 2.95% of reference with a coverageData >= 25X There is a 2.72% of reference with a coverageData >= 26X There is a 2.5% of reference with a coverageData >= 27X There is a 2.31% of reference with a coverageData >= 28X There is a 2.14% of reference with a coverageData >= 29X There is a 1.98% of reference with a coverageData >= 30X There is a 1.83% of reference with a coverageData >= 31X There is a 1.7% of reference with a coverageData >= 32X There is a 1.58% of reference with a coverageData >= 33X There is a 1.46% of reference with a coverageData >= 34X There is a 1.36% of reference with a coverageData >= 35X There is a 1.27% of reference with a coverageData >= 36X There is a 1.18% of reference with a coverageData >= 37X There is a 1.1% of reference with a coverageData >= 38X There is a 1.03% of reference with a coverageData >= 39X There is a 0.96% of reference with a coverageData >= 40X There is a 0.9% of reference with a coverageData >= 41X There is a 0.84% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.74% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.51% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1142083951 4.582070634038661 57.259824942746924 chr2 243199373 1128740183 4.641213375990077 64.61521430477124 chr3 198022430 920802200 4.649989397665709 10.167400008073429 chr4 191154276 705534832 3.6909183867799014 71.7316290928289 chr5 180915260 730641752 4.038585534465141 10.019767536141972 chr6 171115067 665150098 3.88715096608062 22.05523108052623 chr7 159138663 917375341 5.7646289324423945 51.610849152754355 chr8 146364022 872914570 5.963996876226864 18.882230044354674 chr9 141213431 513793707 3.638419542401742 76.21074062521099 chr10 135534747 724257242 5.343701582296088 197.4742430198941 chr11 135006516 459226628 3.4015145461571645 18.794046988274832 chr12 133851895 624696580 4.667073110918602 19.32246123166898 chr13 115169878 324689377 2.819221333203114 6.600169005365961 chr14 107349540 379380165 3.534064188817204 10.046742244490108 chr15 102531392 321595208 3.1365536127706135 11.379809405490688 chr16 90354753 489002146 5.412024600410341 91.50194740021503 chr17 81195210 273598328 3.3696363122898507 51.04199167770877 chr18 78077248 209805891 2.68715786447801 59.876281125865276 chr19 59128983 196473777 3.3227998695665035 29.560933657101266 chr20 63025520 267644071 4.24659837792691 23.405526072744838 chr21 48129895 140498460 2.9191516000606277 33.738302563895544 chr22 51304566 110604259 2.1558365584848724 8.476941798935718 chrMT 16571 9213067 555.9753183271981 290.26188512648264 chrX 155270560 635796561 4.094765685136964 14.738114605619344 chrY 59373566 283282801 4.771193985552426 122.1023566546786