BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004125.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 = 2,552,071 number of mapped reads = 2,309,520 (90.5%) number of supplementary alignments = 16,868 (0.66%) number of secondary alignments = 0 number of mapped bases = 147,633,032 bp number of sequenced bases = 147,562,796 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,489 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5505 >>>>>>> ACTG content number of A's = 38,906,190 bp (26.37%) number of C's = 28,674,849 bp (19.43%) number of T's = 44,108,885 bp (29.89%) number of G's = 35,853,726 bp (24.3%) number of N's = 19,146 bp (0.01%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,376,751 number of insertions = 12,637 mapped reads with insertion percentage = 0.54% number of deletions = 42,161 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.5124X There is a 3.79% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16016827 0.06425992816282693 0.7883069463327862 chr2 243199373 15146329 0.062279473886637036 0.8788482966160045 chr3 198022430 10536767 0.05320996717392065 0.2798513043083415 chr4 191154276 6630946 0.03468897551629972 0.24026404425185602 chr5 180915260 7733688 0.04274757143206162 0.25762899406296613 chr6 171115067 9690731 0.05663283292288925 0.38730328337533254 chr7 159138663 7531870 0.04732897624004796 0.548818875368544 chr8 146364022 9207699 0.06290957896743231 0.5220285730244161 chr9 141213431 5106079 0.036158593158181956 0.5419126186707075 chr10 135534747 6078201 0.044846071834258115 0.3700317167174435 chr11 135006516 5487360 0.04064514930523798 0.432736803090757 chr12 133851895 5750763 0.04296362782163077 0.26523780760253524 chr13 115169878 2946660 0.02558533577677316 0.18903430201366891 chr14 107349540 2922667 0.027225705857705586 0.33479109042002625 chr15 102531392 3359333 0.032763946089798525 0.22988750141725448 chr16 90354753 5852765 0.06477539703971079 0.35286414507242975 chr17 81195210 3936103 0.04847703454427915 0.34272194625285857 chr18 78077248 5000279 0.06404271574735831 1.2141120200159103 chr19 59128983 3621919 0.061254545845985546 0.682980488392849 chr20 63025520 3219077 0.05107577057674415 0.3191059089449239 chr21 48129895 2997422 0.06227775896872412 0.3322866309424605 chr22 51304566 2523240 0.049181587463384836 0.27490872963745444 chrMT 16571 103925 6.271498400820711 7.699455979755246 chrX 155270560 5918914 0.03812000162812577 0.35678833230543594 chrY 59373566 313468 0.005279588563031568 0.11096124599294066