BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472436.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 = 18,819,380 number of mapped reads = 18,628,313 (98.98%) number of supplementary alignments = 77,630 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,350,412 number of mapped paired reads (second in pair) = 9,277,901 number of mapped paired reads (both in pair) = 18,518,172 number of mapped paired reads (singletons) = 110,141 number of mapped bases = 1,827,587,967 bp number of sequenced bases = 1,827,358,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,971,333 duplication rate = 47.24% >>>>>>> Insert size mean insert size = 19,189.241 std insert size = 1,334,011.2978 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 54.7288 >>>>>>> ACTG content number of A's = 510,365,848 bp (27.93%) number of C's = 404,835,220 bp (22.15%) number of T's = 510,059,299 bp (27.91%) number of G's = 401,871,218 bp (21.99%) number of N's = 226,560 bp (0.01%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,462,760 number of insertions = 119,859 mapped reads with insertion percentage = 0.64% number of deletions = 96,414 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.5904X std coverageData = 20.8822X There is a 4.96% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158470608 0.6357882173541305 20.453725021484345 chr2 243199373 157948815 0.6494622623883163 21.85034811140962 chr3 198022430 128865796 0.6507636331904421 15.558141358866727 chr4 191154276 49529721 0.25910862177103483 8.885272200182285 chr5 180915260 91996567 0.5085063968622658 23.073005167323757 chr6 171115067 121866759 0.7121918667746541 15.861987007933479 chr7 159138663 103159085 0.6482339555661593 20.18475836204265 chr8 146364022 161286378 1.1019537164672886 25.887186095288584 chr9 141213431 59801345 0.423481991596111 10.882340002610189 chr10 135534747 35686850 0.2633040662259103 10.579742529996613 chr11 135006516 61753450 0.45741088526423423 20.279760392839794 chr12 133851895 81063699 0.6056223484919657 14.77320465036768 chr13 115169878 120859083 1.0493983765442558 45.019730987434535 chr14 107349540 28455898 0.2650770371256365 7.902055986209171 chr15 102531392 32919383 0.32106638130885806 11.297950604247582 chr16 90354753 74308426 0.8224074941580549 19.57321016568012 chr17 81195210 87581182 1.0786496149218654 27.047869082378313 chr18 78077248 8549238 0.10949717387580055 3.3457486603964406 chr19 59128983 27692840 0.46834629305225833 13.26773205303774 chr20 63025520 68773245 1.09119678822166 35.05574793259206 chr21 48129895 13226824 0.2748151434778738 12.519040694436592 chr22 51304566 11827942 0.23054365180674172 6.811622662862956 chrMT 16571 1704 0.10283024560980025 0.4218388999833095 chrX 155270560 141586884 0.9118720509541538 36.02057031811542 chrY 59373566 376245 0.0063369109411417195 0.37556359097255015