BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238498.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,757,350 number of mapped reads = 5,051,220 (87.74%) number of supplementary alignments = 41,162 (0.71%) number of secondary alignments = 0 number of mapped bases = 309,246,440 bp number of sequenced bases = 309,080,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,685,802 duplication rate = 20.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9463 >>>>>>> ACTG content number of A's = 76,063,780 bp (24.61%) number of C's = 54,040,414 bp (17.48%) number of T's = 104,283,162 bp (33.74%) number of G's = 74,672,537 bp (24.16%) number of N's = 20,222 bp (0.01%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,982,823 number of insertions = 20,737 mapped reads with insertion percentage = 0.41% number of deletions = 98,556 mapped reads with deletion percentage = 1.93% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.0999X std coverageData = 1.5517X There is a 3.97% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 1.27% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27111593 0.10877241906651057 1.7291656518403764 chr2 243199373 33591797 0.13812452139833437 3.8580705337920516 chr3 198022430 16582100 0.08373849366458133 0.6408969574757578 chr4 191154276 30229747 0.15814319005869373 0.8557091400914779 chr5 180915260 13855102 0.07658337942305143 0.6198819270727629 chr6 171115067 21442837 0.12531238409297996 1.5000002442148541 chr7 159138663 22341918 0.14039277180555426 1.938976422689924 chr8 146364022 19586938 0.13382344740430815 1.1272847085750721 chr9 141213431 7092959 0.05022864291145224 0.9341485302760169 chr10 135534747 7614126 0.05617840567481931 0.8245287045013845 chr11 135006516 14723754 0.10905958050202555 0.8653174097769105 chr12 133851895 18416440 0.13758819029046992 0.844311053207609 chr13 115169878 4488068 0.03896911308701742 0.7582439972321401 chr14 107349540 3053232 0.028441966309310687 0.5487012246107623 chr15 102531392 4775985 0.04658070964256488 0.7624625542670374 chr16 90354753 9716040 0.10753214056154854 0.8767699601753149 chr17 81195210 3656802 0.04503716413813081 0.46034766554233486 chr18 78077248 14548236 0.18633131126752828 2.8942284256687643 chr19 59128983 6698087 0.11327925257906094 1.401076055825477 chr20 63025520 5615151 0.0890932910985899 0.7589954771316012 chr21 48129895 8807825 0.18300112643088043 0.9661461679351481 chr22 51304566 3949226 0.0769761116388744 0.5969580399629819 chrMT 16571 100422 6.060105002715588 5.822427232987389 chrX 155270560 10376969 0.06683152942837328 0.7206897543376378 chrY 59373566 871086 0.014671276439754351 0.4985543156164084