BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013258.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 = 2,211,855 number of mapped reads = 1,979,507 (89.5%) number of supplementary alignments = 13,180 (0.6%) number of secondary alignments = 0 number of mapped bases = 131,323,854 bp number of sequenced bases = 131,253,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,832 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4493 >>>>>>> ACTG content number of A's = 36,713,287 bp (27.97%) number of C's = 23,753,517 bp (18.1%) number of T's = 42,014,426 bp (32.01%) number of G's = 28,770,552 bp (21.92%) number of N's = 1,891 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,009,607 number of insertions = 9,206 mapped reads with insertion percentage = 0.46% number of deletions = 40,748 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.49% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.4631X There is a 3.54% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% 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 12439548 0.04990779140325592 1.0601062123647795 chr2 243199373 19030551 0.07825082262855998 0.5762574787910528 chr3 198022430 6665127 0.0336584446519518 0.21111463587683765 chr4 191154276 5169356 0.027042847840871735 0.19653980063045629 chr5 180915260 7594328 0.041977266041571065 0.24025445470876838 chr6 171115067 6779105 0.03961723019983974 0.3617193053551046 chr7 159138663 10245189 0.06437900637634489 0.6469616357880698 chr8 146364022 7739459 0.052878151981912605 0.4177252856354252 chr9 141213431 4242264 0.030041505046357806 0.37518140779424153 chr10 135534747 4088802 0.03016792439211179 0.3136161688143002 chr11 135006516 5367306 0.03975590333728781 0.2936807004294293 chr12 133851895 3651304 0.027278687388026895 0.19610135494115222 chr13 115169878 4607184 0.04000337657733735 0.2283211739357565 chr14 107349540 3112985 0.02899858723195274 0.20602067637602542 chr15 102531392 1819694 0.01774767673104448 0.15786243520010254 chr16 90354753 6062890 0.06710095261950415 0.3172119908634173 chr17 81195210 3541374 0.04361555318349444 0.32824726080929434 chr18 78077248 3644830 0.04668235745194298 0.5898461791396407 chr19 59128983 2501236 0.04230135329741761 0.7282539543863622 chr20 63025520 3882551 0.061602839611636685 0.2901660859676606 chr21 48129895 3107685 0.06456870516754712 0.30584467002771093 chr22 51304566 1046059 0.020389198887288122 0.16155369257906144 chrMT 16571 15020 0.906402751795305 1.1796626431975354 chrX 155270560 4693221 0.030226084068995435 0.24768574190594267 chrY 59373566 276786 0.00466177153651172 0.11031899997996014