BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472391.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,484,628 number of mapped reads = 18,282,857 (98.91%) number of supplementary alignments = 75,049 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,173,942 number of mapped paired reads (second in pair) = 9,108,915 number of mapped paired reads (both in pair) = 18,162,302 number of mapped paired reads (singletons) = 120,555 number of mapped bases = 1,796,021,256 bp number of sequenced bases = 1,795,808,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,078,942 duplication rate = 46.84% >>>>>>> Insert size mean insert size = 23,959.9048 std insert size = 1,505,999.945 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.8058 >>>>>>> ACTG content number of A's = 489,272,762 bp (27.25%) number of C's = 410,249,064 bp (22.84%) number of T's = 489,394,786 bp (27.25%) number of G's = 406,671,627 bp (22.65%) number of N's = 220,120 bp (0.01%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,591,523 number of insertions = 107,477 mapped reads with insertion percentage = 0.58% number of deletions = 90,015 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.5802X std coverageData = 16.4748X There is a 5.13% of reference with a coverageData >= 1X There is a 2.12% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 160865087 0.6453949296278785 18.945104342794338 chr2 243199373 131116871 0.539133260841096 14.870716024687185 chr3 198022430 123237548 0.6223413579966673 13.07790622083278 chr4 191154276 52132708 0.2727258269650217 9.842899986182072 chr5 180915260 53329002 0.2947733762204471 7.946835962223162 chr6 171115067 157282920 0.9191646460916267 20.965133185680777 chr7 159138663 127828331 0.8032512564215775 19.58442774115278 chr8 146364022 107345676 0.7334157297207916 20.304545511214332 chr9 141213431 63723764 0.4512585208697323 10.536289910405982 chr10 135534747 50195159 0.370349007254944 10.786822426714112 chr11 135006516 57939712 0.42916233761635625 12.084467764178894 chr12 133851895 92337587 0.6898489334050892 17.351947979021762 chr13 115169878 71995164 0.6251214749050963 22.75170008299344 chr14 107349540 46232138 0.4306691765982416 11.74059246145433 chr15 102531392 48872707 0.4766609137619043 28.181238117777326 chr16 90354753 99555786 1.10183230759316 24.038007266090574 chr17 81195210 76461302 0.9416972011033656 20.00759767667188 chr18 78077248 22167654 0.283919510072896 9.946360247260992 chr19 59128983 37044596 0.626504873253105 10.774706846629071 chr20 63025520 63403708 1.0060005534266119 23.28026767501707 chr21 48129895 13323261 0.2768188253890851 12.03946156867293 chr22 51304566 14580868 0.28420215074034544 7.636758913493483 chrMT 16571 29179 1.760847263291292 1.9360632844809842 chrX 155270560 124654963 0.8028241992558023 17.15145463455074 chrY 59373566 365565 0.006157032912592786 0.33908262107707515