BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708637.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,762,812 number of mapped reads = 4,407,836 (92.55%) number of supplementary alignments = 116 (0%) number of secondary alignments = 0 number of mapped bases = 219,866,351 bp number of sequenced bases = 219,844,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,292 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5123 >>>>>>> ACTG content number of A's = 67,905,765 bp (30.89%) number of C's = 41,831,703 bp (19.03%) number of T's = 67,804,685 bp (30.84%) number of G's = 42,294,472 bp (19.24%) number of N's = 7,728 bp (0%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 359,817 number of insertions = 13,902 mapped reads with insertion percentage = 0.31% number of deletions = 12,651 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.071X std coverageData = 0.2782X There is a 6.58% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 17520780 0.0702938268707463 0.2777517590462925 chr2 243199373 17716331 0.07284694356510532 0.27966931252298355 chr3 198022430 17505599 0.088402101721507 0.3087474305338422 chr4 191154276 17156319 0.08975116517927122 0.3120260760528712 chr5 180915260 15306904 0.08460814195552105 0.3022563014815694 chr6 171115067 14505079 0.08476798247111693 0.3033919134743617 chr7 159138663 12089011 0.07596526684404782 0.2865678869447262 chr8 146364022 12480673 0.085271454210243 0.30326435140757707 chr9 141213431 9057782 0.0641424964740075 0.26460009494337866 chr10 135534747 9104191 0.06717237609924487 0.2686231101639617 chr11 135006516 9652245 0.07149466030217386 0.27974669296774907 chr12 133851895 10421185 0.07785608862691111 0.2906249800818961 chr13 115169878 7826363 0.06795494738650326 0.27095949801393204 chr14 107349540 7737875 0.07208111930428393 0.2816294734142412 chr15 102531392 4933698 0.048118901965165946 0.2288016368890026 chr16 90354753 3841589 0.04251673401176804 0.21288797693735967 chr17 81195210 3661960 0.0451006900530216 0.22084555975424863 chr18 78077248 9713502 0.12440886748467364 0.3704746388051619 chr19 59128983 1960507 0.0331564471521521 0.18781031510273025 chr20 63025520 3463660 0.05495646842739259 0.2457967618129572 chr21 48129895 2937109 0.06102462928705745 0.2610509285681987 chr22 51304566 1346399 0.026243258738413263 0.1678893203057922 chrMT 16571 400 0.024138555307464848 0.15347926718333427 chrX 155270560 8751672 0.05636401388647017 0.24581184641770534 chrY 59373566 1175518 0.019798676064024856 0.14672627757279874