BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365372.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 558,021,958 number of mapped reads = 536,553,522 (96.15%) number of supplementary alignments = 12,317,754 (2.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 268,484,274 number of mapped paired reads (second in pair) = 268,069,248 number of mapped paired reads (both in pair) = 533,041,450 number of mapped paired reads (singletons) = 3,512,072 number of mapped bases = 75,197,287,182 bp number of sequenced bases = 75,181,721,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,478,023 duplication rate = 38.55% >>>>>>> Insert size mean insert size = 82,691.0016 std insert size = 2,838,544.8737 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 54.3663 >>>>>>> ACTG content number of A's = 20,505,747,173 bp (27.27%) number of C's = 17,137,232,367 bp (22.79%) number of T's = 19,914,087,853 bp (26.49%) number of G's = 17,621,922,403 bp (23.44%) number of N's = 2,732,133 bp (0%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 445,796,094 number of insertions = 6,981,092 mapped reads with insertion percentage = 1.27% number of deletions = 5,449,245 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 24.2909X std coverageData = 54.2649X There is a 73.17% of reference with a coverageData >= 1X There is a 69.81% of reference with a coverageData >= 2X There is a 63.19% of reference with a coverageData >= 3X There is a 60.33% of reference with a coverageData >= 4X There is a 56.15% of reference with a coverageData >= 5X There is a 53.65% of reference with a coverageData >= 6X There is a 50.63% of reference with a coverageData >= 7X There is a 48.47% of reference with a coverageData >= 8X There is a 46.12% of reference with a coverageData >= 9X There is a 44.25% of reference with a coverageData >= 10X There is a 42.32% of reference with a coverageData >= 11X There is a 40.7% of reference with a coverageData >= 12X There is a 39.07% of reference with a coverageData >= 13X There is a 37.64% of reference with a coverageData >= 14X There is a 36.23% of reference with a coverageData >= 15X There is a 34.97% of reference with a coverageData >= 16X There is a 33.74% of reference with a coverageData >= 17X There is a 32.61% of reference with a coverageData >= 18X There is a 31.52% of reference with a coverageData >= 19X There is a 30.5% of reference with a coverageData >= 20X There is a 29.53% of reference with a coverageData >= 21X There is a 28.61% of reference with a coverageData >= 22X There is a 27.73% of reference with a coverageData >= 23X There is a 26.9% of reference with a coverageData >= 24X There is a 26.1% of reference with a coverageData >= 25X There is a 25.34% of reference with a coverageData >= 26X There is a 24.62% of reference with a coverageData >= 27X There is a 23.92% of reference with a coverageData >= 28X There is a 23.26% of reference with a coverageData >= 29X There is a 22.62% of reference with a coverageData >= 30X There is a 22.01% of reference with a coverageData >= 31X There is a 21.42% of reference with a coverageData >= 32X There is a 20.86% of reference with a coverageData >= 33X There is a 20.32% of reference with a coverageData >= 34X There is a 19.8% of reference with a coverageData >= 35X There is a 19.3% of reference with a coverageData >= 36X There is a 18.81% of reference with a coverageData >= 37X There is a 18.35% of reference with a coverageData >= 38X There is a 17.9% of reference with a coverageData >= 39X There is a 17.46% of reference with a coverageData >= 40X There is a 17.04% of reference with a coverageData >= 41X There is a 16.64% of reference with a coverageData >= 42X There is a 16.25% of reference with a coverageData >= 43X There is a 15.87% of reference with a coverageData >= 44X There is a 15.51% of reference with a coverageData >= 45X There is a 15.15% of reference with a coverageData >= 46X There is a 14.81% of reference with a coverageData >= 47X There is a 14.48% of reference with a coverageData >= 48X There is a 14.16% of reference with a coverageData >= 49X There is a 13.85% of reference with a coverageData >= 50X There is a 13.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7106231263 28.510385388367798 65.4258023443263 chr2 243199373 6468568720 26.597801796141965 67.30712807937209 chr3 198022430 3886106413 19.624576938077166 40.31744553370701 chr4 191154276 2084883454 10.906810444564682 33.060661301874674 chr5 180915260 4771418122 26.373773677245357 51.88563253734806 chr6 171115067 4513428225 26.37656814288598 49.64032680291546 chr7 159138663 4375817914 27.496887503698584 49.91268694649355 chr8 146364022 5088295238 34.76465847597438 65.33430167166452 chr9 141213431 2765946658 19.58699422861555 48.12799347037879 chr10 135534747 4506489469 33.249698462933644 61.21034668904962 chr11 135006516 4593399446 34.0235388786716 66.8290064974766 chr12 133851895 3796872143 28.366218819688733 55.7095448454057 chr13 115169878 2753879690 23.911457907422633 48.380115645576964 chr14 107349540 2335356070 21.7546909842371 46.12774673852279 chr15 102531392 1640261827 15.9976549133362 39.08395831200388 chr16 90354753 2494565040 27.608564654036517 59.24581783212727 chr17 81195210 1663605664 20.48896312972157 50.619155217739184 chr18 78077248 1639992998 21.004749014719373 56.29612222167763 chr19 59128983 1689530555 28.57364475556767 63.00607005744479 chr20 63025520 1875502353 29.75782433845845 63.91099865732407 chr21 48129895 1219813433 25.344194767098493 58.70676069709537 chr22 51304566 1091353264 21.27204943123386 49.36194570063753 chrMT 16571 10583576 638.680586566894 275.9141743261145 chrX 155270560 2420342664 15.587904519697746 38.24767950077747 chrY 59373566 405042983 6.821941316443752 29.46999921243181