BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234020.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 = 768,038 number of mapped reads = 538,784 (70.15%) number of supplementary alignments = 5,243 (0.68%) number of secondary alignments = 0 number of mapped bases = 34,732,451 bp number of sequenced bases = 34,710,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,757 duplication rate = 7.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.521 >>>>>>> ACTG content number of A's = 9,597,866 bp (27.65%) number of C's = 5,799,863 bp (16.71%) number of T's = 11,747,245 bp (33.84%) number of G's = 7,558,367 bp (21.78%) number of N's = 7,102 bp (0.02%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 304,040 number of insertions = 3,059 mapped reads with insertion percentage = 0.56% number of deletions = 12,430 mapped reads with deletion percentage = 2.28% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0112X std coverageData = 0.2193X There is a 0.8% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% 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 3894963 0.015626693263083184 0.2740319465067664 chr2 243199373 2821219 0.01160043697974501 0.19559410745212644 chr3 198022430 2281117 0.011519487969115418 0.1428592923528706 chr4 191154276 1338307 0.007001187878214139 0.11458632886155043 chr5 180915260 1902249 0.010514585668450522 0.13812349387070613 chr6 171115067 2593759 0.015157981383369356 0.17846307892290034 chr7 159138663 2638436 0.016579478237793162 0.20433103010148432 chr8 146364022 2233209 0.01525790948816643 0.6747320152791736 chr9 141213431 1340718 0.009494266873240974 0.1457396546932298 chr10 135534747 834096 0.0061541119046025885 0.10940651136278261 chr11 135006516 1704876 0.012628101594740804 0.17300895730289859 chr12 133851895 1105287 0.008257537183168007 0.12251982463117402 chr13 115169878 1540035 0.013371855790278775 0.15752941059788042 chr14 107349540 1918879 0.017875055636009246 0.18491110144844913 chr15 102531392 533565 0.005203918425295543 0.09469324759893201 chr16 90354753 910086 0.010072364427801602 0.1358134530581171 chr17 81195210 849705 0.010464964620449902 0.13511186616883528 chr18 78077248 735130 0.009415418945093967 0.22288201458366494 chr19 59128983 844097 0.014275520348455849 0.18629009029476745 chr20 63025520 706899 0.011216075646817352 0.14029950587251153 chr21 48129895 634958 0.01319259059260362 0.15625523971257888 chr22 51304566 321600 0.006268447919430797 0.09949156233637359 chrMT 16571 23721 1.431476676120934 1.8556450052458502 chrX 155270560 945898 0.006091933976408664 0.10616339406250297 chrY 59373566 79642 0.0013413713436043239 0.04714479557926967