BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240257.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 = 1,175,084 number of mapped reads = 886,372 (75.43%) number of supplementary alignments = 3,428 (0.29%) number of secondary alignments = 0 number of mapped bases = 56,123,892 bp number of sequenced bases = 56,092,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,657 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1378 >>>>>>> ACTG content number of A's = 16,023,103 bp (28.57%) number of C's = 9,731,087 bp (17.35%) number of T's = 17,617,687 bp (31.41%) number of G's = 12,707,404 bp (22.65%) number of N's = 13,624 bp (0.02%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 568,334 number of insertions = 4,109 mapped reads with insertion percentage = 0.46% number of deletions = 17,922 mapped reads with deletion percentage = 2% homopolymer indels = 48.92% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.2077X There is a 1.63% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4236360 0.016996386941800237 0.32911931630913294 chr2 243199373 5407130 0.022233322122915178 0.24570072467728118 chr3 198022430 3935697 0.019875006078856824 0.15301708362726613 chr4 191154276 3631210 0.01899622690103987 0.15222079297272906 chr5 180915260 3459949 0.019124694069477612 0.15087205861358896 chr6 171115067 3196778 0.01868203692431129 0.17277971338071435 chr7 159138663 3235040 0.020328435208733658 0.3080808489551069 chr8 146364022 3133478 0.02140879949308854 0.29837506439895484 chr9 141213431 2172437 0.01538406782284045 0.1910583121376156 chr10 135534747 2501168 0.018454072150221375 0.16793870237638692 chr11 135006516 2604029 0.019288172727900038 0.1940315386832714 chr12 133851895 2679633 0.02001938784654487 0.15580435702705078 chr13 115169878 1417109 0.012304510733266558 0.1195229229846528 chr14 107349540 1964794 0.018302770556818407 0.15258401997667093 chr15 102531392 1396198 0.013617273429780414 0.13071989676007462 chr16 90354753 1524864 0.016876411581801348 0.14713569858381478 chr17 81195210 1304174 0.01606220366940365 0.14813978749008927 chr18 78077248 1499212 0.01920165014012789 0.3111840085180018 chr19 59128983 932396 0.01576884892473121 0.2265414245255944 chr20 63025520 1148858 0.018228457297932647 0.15053330805204537 chr21 48129895 932402 0.019372616541133116 0.1565895994486644 chr22 51304566 481172 0.009378736387712548 0.10428545712787506 chrMT 16571 15679 0.9461710216643534 1.2159360383329183 chrX 155270560 3187967 0.020531689973939685 0.16894475729690223 chrY 59373566 126158 0.0021248176334902977 0.05363257286974679