BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004029.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 = 1,982,898 number of mapped reads = 1,776,121 (89.57%) number of supplementary alignments = 13,724 (0.69%) number of secondary alignments = 0 number of mapped bases = 118,571,056 bp number of sequenced bases = 118,504,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,312 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.485 >>>>>>> ACTG content number of A's = 33,488,254 bp (28.26%) number of C's = 21,744,672 bp (18.35%) number of T's = 37,363,909 bp (31.53%) number of G's = 25,888,827 bp (21.85%) number of N's = 18,680 bp (0.02%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,117,010 number of insertions = 9,224 mapped reads with insertion percentage = 0.52% number of deletions = 39,966 mapped reads with deletion percentage = 2.22% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3445X There is a 3.36% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9626357 0.03862119565190572 0.5960733524419579 chr2 243199373 8244352 0.03389956108151644 0.32582620871241935 chr3 198022430 6306266 0.031846220652882604 0.1977533960056994 chr4 191154276 8899428 0.04655625909200169 0.24323212077426412 chr5 180915260 8999959 0.04974682069384307 0.24741613567148668 chr6 171115067 6418677 0.03751088149356246 0.24227156358961127 chr7 159138663 7130109 0.04480437918471138 0.6148334594928689 chr8 146364022 10969546 0.07494701122657042 0.539198523084074 chr9 141213431 4208760 0.029804247161164154 0.2723728935074635 chr10 135534747 5660622 0.04176509806743506 0.347050805917895 chr11 135006516 4656682 0.03449227591355665 0.2448671498146514 chr12 133851895 5691848 0.04252347716108166 0.23031781925425301 chr13 115169878 4720489 0.040987184166332104 0.22542474690347838 chr14 107349540 3336266 0.031078530937347287 0.21492387761918294 chr15 102531392 3524008 0.034370039567979335 0.20545465547965341 chr16 90354753 3158466 0.03495627949976245 0.23528677145185511 chr17 81195210 2651801 0.03265957437637023 0.20909345868443935 chr18 78077248 2686864 0.03441289324131916 0.5088117274711561 chr19 59128983 1868091 0.03159349113107526 0.41550401191882763 chr20 63025520 2188123 0.034718047546454196 0.21698908852395357 chr21 48129895 1530526 0.031799903157902175 0.20914822590758242 chr22 51304566 1108807 0.021612247923508406 0.16007522849946976 chrMT 16571 38819 2.342586446201195 2.17116833269142 chrX 155270560 4713945 0.030359554316027455 0.2072154068772151 chrY 59373566 232245 0.00391158920789767 0.09222750786948389