BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238247.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 = 2,003,235 number of mapped reads = 1,818,950 (90.8%) number of supplementary alignments = 19,544 (0.98%) number of secondary alignments = 0 number of mapped bases = 118,636,855 bp number of sequenced bases = 118,579,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,114 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3116 >>>>>>> ACTG content number of A's = 33,568,856 bp (28.31%) number of C's = 23,163,410 bp (19.53%) number of T's = 35,935,574 bp (30.31%) number of G's = 25,892,160 bp (21.84%) number of N's = 19,562 bp (0.02%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,004,552 number of insertions = 9,436 mapped reads with insertion percentage = 0.51% number of deletions = 34,655 mapped reads with deletion percentage = 1.88% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3205X There is a 3.27% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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 12457636 0.04998036093157818 0.5717817814426936 chr2 243199373 9229696 0.03795115047438877 0.3591728549691454 chr3 198022430 5934117 0.029966893144377633 0.19616424498898882 chr4 191154276 7486681 0.0391656475421978 0.22894507645573375 chr5 180915260 4444579 0.024567186869698002 0.17838320602297103 chr6 171115067 5382354 0.031454588391097084 0.23157710445854593 chr7 159138663 8462872 0.053179232755021955 0.48254563769988434 chr8 146364022 3339838 0.02281870882176222 0.34776805065851324 chr9 141213431 1263314 0.008946132043204871 0.17023345271694915 chr10 135534747 5996033 0.04423982139428791 0.3217581857649392 chr11 135006516 8094656 0.059957520865141056 0.3753838691411145 chr12 133851895 7187755 0.05369931445498026 0.2641641558926189 chr13 115169878 1342510 0.011656780603692227 0.12415808546214452 chr14 107349540 1386481 0.01291557467316581 0.13493672369721663 chr15 102531392 5382503 0.052496146741087844 0.26569765445502375 chr16 90354753 4685537 0.05185711702404853 0.27252216533647855 chr17 81195210 4138723 0.0509725019493145 0.29055750184694606 chr18 78077248 3517500 0.04505153665252136 0.3749174461540122 chr19 59128983 3176514 0.05372177634105427 0.43987873210806927 chr20 63025520 1903105 0.030195784183930572 0.20050313660563257 chr21 48129895 1628828 0.033842334374508815 0.21524759753768938 chr22 51304566 1697544 0.033087581327556695 0.20628406545961542 chrMT 16571 8639 0.5213324482529721 0.8541372241215768 chrX 155270560 10166393 0.06547534188065014 0.31839474276160795 chrY 59373566 323047 0.005440922985828408 0.1264076087393579