BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004041.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 = 2,919,478 number of mapped reads = 2,578,616 (88.32%) number of supplementary alignments = 28,580 (0.98%) number of secondary alignments = 0 number of mapped bases = 171,266,947 bp number of sequenced bases = 171,190,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,886 duplication rate = 4.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1153 >>>>>>> ACTG content number of A's = 47,350,753 bp (27.66%) number of C's = 32,372,107 bp (18.91%) number of T's = 53,147,265 bp (31.05%) number of G's = 38,299,995 bp (22.37%) number of N's = 20,660 bp (0.01%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,258,319 number of insertions = 12,042 mapped reads with insertion percentage = 0.46% number of deletions = 43,693 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.43X There is a 4.3% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 13491743 0.05412922521866054 0.7317565098379188 chr2 243199373 13082807 0.053794575366771194 0.47364290291799527 chr3 198022430 10530966 0.053180672512704745 0.2820267612724862 chr4 191154276 11278859 0.059003958666349686 0.31797212124556584 chr5 180915260 11115282 0.06143916218012787 0.30643977064324596 chr6 171115067 11000417 0.06428666506614522 0.3507609642944623 chr7 159138663 8321069 0.05228816708105685 0.557007715819517 chr8 146364022 12455863 0.08510194534009184 0.6595956120165178 chr9 141213431 6419602 0.04546027919964638 0.3776670697008643 chr10 135534747 7910997 0.058368773876119016 0.39766111765803414 chr11 135006516 6354243 0.04706619493832431 0.3499881422139691 chr12 133851895 8023581 0.05994372362079745 0.30721969884715694 chr13 115169878 5801242 0.050371174310004915 0.27582854626304404 chr14 107349540 4364977 0.040661347966651745 0.27326293141464536 chr15 102531392 6638161 0.06474271801557127 0.3159990663762255 chr16 90354753 4816695 0.05330870640529558 0.30781716484626653 chr17 81195210 4208736 0.05183478187937441 0.30318690008848725 chr18 78077248 4654776 0.059617572586574775 0.6539034502891521 chr19 59128983 2709422 0.0458222323898248 0.5512344974035887 chr20 63025520 3269068 0.05186895720971441 0.2930351402691917 chr21 48129895 2278303 0.047336546235972464 0.28716858766921555 chr22 51304566 1491933 0.029079926336381054 0.2059834807113349 chrMT 16571 10020 0.6046708104519944 1.0725202796766093 chrX 155270560 10633938 0.06848650510438038 0.3561993523519186 chrY 59373566 404247 0.006808534963185469 0.14524880210327976