BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240233.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 = 1,405,683 number of mapped reads = 1,094,357 (77.85%) number of supplementary alignments = 8,330 (0.59%) number of secondary alignments = 0 number of mapped bases = 70,569,023 bp number of sequenced bases = 70,535,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,848 duplication rate = 9.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3484 >>>>>>> ACTG content number of A's = 19,199,155 bp (27.22%) number of C's = 12,782,339 bp (18.12%) number of T's = 22,753,119 bp (32.26%) number of G's = 15,781,562 bp (22.37%) number of N's = 19,001 bp (0.03%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 585,476 number of insertions = 4,735 mapped reads with insertion percentage = 0.43% number of deletions = 19,498 mapped reads with deletion percentage = 1.76% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.2665X There is a 1.43% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 5557158 0.022295463007091162 0.3680665362539654 chr2 243199373 7288403 0.029968839598940908 0.3296815171041456 chr3 198022430 4656253 0.02351376558706001 0.22770833691435907 chr4 191154276 4475069 0.023410771098837466 0.2280891437337285 chr5 180915260 3819413 0.021111613249208495 0.216133748563831 chr6 171115067 3872505 0.022630999525015526 0.23910923141924503 chr7 159138663 4057092 0.0254940686538255 0.3468458079139455 chr8 146364022 3875766 0.02648031904999167 0.3176424752751108 chr9 141213431 2740965 0.019410087132575936 0.24196605454308232 chr10 135534747 3275216 0.024165138995684995 0.2577499942851729 chr11 135006516 3125572 0.023151267750661755 0.2535162899223155 chr12 133851895 3471817 0.025937750078174088 0.24135610550483488 chr13 115169878 1867296 0.016213406078280295 0.1890478662807265 chr14 107349540 2281077 0.021249061709998945 0.2200070754581561 chr15 102531392 2022320 0.019723910507330283 0.20937084761653696 chr16 90354753 2081343 0.023035235346169337 0.22986661641040773 chr17 81195210 1754153 0.021604143889768865 0.22028692085671694 chr18 78077248 1694689 0.021705286026474705 0.3490319423875919 chr19 59128983 1281531 0.021673482867107657 0.2777873595244489 chr20 63025520 1477644 0.02344516951228645 0.23067648304675134 chr21 48129895 1098257 0.022818603697348602 0.22708626742501345 chr22 51304566 664369 0.012949510185896514 0.16902446238275118 chrMT 16571 18128 1.0939593265343068 1.8683750047858936 chrX 155270560 3914068 0.02520804974233364 0.24283710653193502 chrY 59373566 198919 0.003350295651772036 0.07959048211793796