BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013210.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 = 2,841,384 number of mapped reads = 2,474,770 (87.1%) number of supplementary alignments = 22,710 (0.8%) number of secondary alignments = 0 number of mapped bases = 165,272,300 bp number of sequenced bases = 165,209,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,460 duplication rate = 5.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8129 >>>>>>> ACTG content number of A's = 45,225,584 bp (27.37%) number of C's = 30,604,081 bp (18.52%) number of T's = 52,525,626 bp (31.79%) number of G's = 36,817,776 bp (22.29%) number of N's = 36,064 bp (0.02%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,350,347 number of insertions = 11,178 mapped reads with insertion percentage = 0.45% number of deletions = 36,974 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.0534X std coverageData = 0.6344X There is a 4.15% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 17126589 0.06871232228544778 1.3030492139093917 chr2 243199373 12703131 0.05223340357871729 0.6347856617269712 chr3 198022430 8751590 0.044194942966814414 0.25557122647303904 chr4 191154276 15506588 0.08112080108529719 0.35904196649701886 chr5 180915260 9355084 0.05170975626931636 0.27600105538879266 chr6 171115067 9626109 0.056255180614808165 0.3725742296651574 chr7 159138663 14312526 0.08993745284890323 1.3662576813301985 chr8 146364022 13626467 0.09309983979532893 0.7908125549951287 chr9 141213431 1711873 0.012122593353035945 0.373986569905 chr10 135534747 5665954 0.04180443853265171 0.537652602664131 chr11 135006516 7430755 0.05503997303359787 0.39705239234788836 chr12 133851895 10206386 0.07625133734565356 0.34673248758799274 chr13 115169878 4058886 0.03524260050010646 0.22914370617292595 chr14 107349540 7051643 0.06568861869366184 0.335594107186986 chr15 102531392 963019 0.009392430759157156 0.12183816232535442 chr16 90354753 4124892 0.04565218611133827 0.2960394463036927 chr17 81195210 2320064 0.028573902327489516 0.21457452563664212 chr18 78077248 2943682 0.03770217413400636 0.8177200385128546 chr19 59128983 1990387 0.03366178308867582 0.9283566124112992 chr20 63025520 2975241 0.0472069250678138 0.28538019379537216 chr21 48129895 3150509 0.06545846401701064 0.31775962085199005 chr22 51304566 1759588 0.034296908388231954 0.2235547541611941 chrMT 16571 76325 4.605938084605636 3.608372964020468 chrX 155270560 7567132 0.04873513691198125 0.3097010273406182 chrY 59373566 267880 0.004511772124315389 0.08976448932880153