BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472429.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 = 14,522,676 number of mapped reads = 14,394,720 (99.12%) number of supplementary alignments = 55,722 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,218,683 number of mapped paired reads (second in pair) = 7,176,037 number of mapped paired reads (both in pair) = 14,325,920 number of mapped paired reads (singletons) = 68,800 number of mapped bases = 1,411,576,535 bp number of sequenced bases = 1,411,405,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,077,391 duplication rate = 46.83% >>>>>>> Insert size mean insert size = 16,323.924 std insert size = 1,262,797.5414 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.5976 >>>>>>> ACTG content number of A's = 384,061,900 bp (27.21%) number of C's = 322,593,545 bp (22.86%) number of T's = 385,683,533 bp (27.33%) number of G's = 318,898,104 bp (22.59%) number of N's = 168,185 bp (0.01%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 7,360,753 number of insertions = 93,475 mapped reads with insertion percentage = 0.64% number of deletions = 75,258 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.456X std coverageData = 16.6615X There is a 4% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% 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 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167776314 0.6731229528210484 22.35631791350668 chr2 243199373 109856550 0.45171395240398093 14.547808538628564 chr3 198022430 86381283 0.436219689860386 11.027228486156925 chr4 191154276 33155797 0.17345045946029478 5.964905804956373 chr5 180915260 45460782 0.25128218592505686 8.00328993715476 chr6 171115067 131151218 0.7664504377045885 19.57620657529901 chr7 159138663 76333589 0.4796671504020365 15.185564393166732 chr8 146364022 144681062 0.9885015458238774 30.50784831905893 chr9 141213431 32526997 0.23033925859361068 7.843891638010031 chr10 135534747 31568080 0.23291503248240836 9.227558142641767 chr11 135006516 60420386 0.4475368137046067 18.612749231728266 chr12 133851895 75033832 0.560573550340845 14.70240922346649 chr13 115169878 59968307 0.5206943694079453 24.958231888418716 chr14 107349540 26483154 0.246700209428005 8.239008904734254 chr15 102531392 25854482 0.25216162090143085 8.387233037008734 chr16 90354753 105590303 1.168619242421038 39.226363961107126 chr17 81195210 46973593 0.57852665200324 12.640704086250055 chr18 78077248 4842685 0.062024278827040626 2.018865726639964 chr19 59128983 34392151 0.5816462461395624 15.792117981748689 chr20 63025520 59828808 0.9492790856783093 25.29779431623979 chr21 48129895 9648909 0.20047641907384173 9.935142931047713 chr22 51304566 8688902 0.1693592340299692 4.838864356566105 chrMT 16571 1634 0.09860599843099391 0.3424115330865652 chrX 155270560 34697298 0.2234634691856589 6.523110898600616 chrY 59373566 260419 0.004386110142011682 0.39378978366509704