BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237850.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 = 1,527,620 number of mapped reads = 1,375,142 (90.02%) number of supplementary alignments = 7,326 (0.48%) number of secondary alignments = 0 number of mapped bases = 92,014,137 bp number of sequenced bases = 91,968,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,025 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2331 >>>>>>> ACTG content number of A's = 25,440,408 bp (27.66%) number of C's = 16,920,198 bp (18.4%) number of T's = 28,725,580 bp (31.23%) number of G's = 20,808,629 bp (22.63%) number of N's = 73,314 bp (0.08%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 706,387 number of insertions = 8,102 mapped reads with insertion percentage = 0.58% number of deletions = 27,593 mapped reads with deletion percentage = 1.98% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.3457X There is a 2.69% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 9669867 0.03879575890805905 0.7129014812356624 chr2 243199373 6888378 0.028323995720169887 0.27858544083441666 chr3 198022430 6632299 0.03349266545209045 0.20553055633455905 chr4 191154276 3431208 0.01794994112504185 0.1618165794528981 chr5 180915260 4346580 0.024025502326337756 0.16635698296069873 chr6 171115067 6969355 0.040729055145097184 0.2791224451177401 chr7 159138663 6571907 0.041296733779898606 0.5645460263932108 chr8 146364022 5391239 0.036834455123131285 0.3243549981505367 chr9 141213431 4495767 0.03183668131397501 0.3139071928374137 chr10 135534747 4627649 0.034143635506251394 0.4480760941860412 chr11 135006516 3873347 0.02869007448499745 0.26831662883613433 chr12 133851895 4430901 0.0331030128486414 0.19951187535395093 chr13 115169878 2647913 0.022991367586583707 0.15993869076770875 chr14 107349540 2323026 0.021639831898674182 0.19121395352126888 chr15 102531392 1401417 0.013668174913688873 0.12396523455020086 chr16 90354753 2135368 0.023633156298927628 0.20885455185262564 chr17 81195210 2100358 0.02586800378987874 0.1929373265944644 chr18 78077248 1322551 0.016939006354322324 0.570663752646278 chr19 59128983 1973680 0.033379231298464915 0.46693484217959597 chr20 63025520 1243549 0.019730880443350567 0.16034795432467353 chr21 48129895 1129644 0.02347073476889987 0.19177860245702538 chr22 51304566 657410 0.012813869237291668 0.1192503843952947 chrMT 16571 29705 1.7925894635206083 1.616882921028394 chrX 155270560 7460036 0.04804539894748882 0.27064656266935283 chrY 59373566 260983 0.0043956093188002214 0.11237215596406232