BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514724.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 160,598,618 number of mapped reads = 152,196,654 (94.77%) number of supplementary alignments = 8,442,198 (5.26%) number of secondary alignments = 0 number of mapped bases = 14,109,267,552 bp number of sequenced bases = 14,096,806,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,571,783 duplication rate = 54.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8997 >>>>>>> ACTG content number of A's = 3,732,983,328 bp (26.48%) number of C's = 3,210,482,711 bp (22.77%) number of T's = 3,772,417,695 bp (26.76%) number of G's = 3,225,239,542 bp (22.88%) number of N's = 155,682,925 bp (1.1%) GC percentage = 45.65% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 132,982,917 number of insertions = 7,430,443 mapped reads with insertion percentage = 4.64% number of deletions = 4,987,459 mapped reads with deletion percentage = 3.1% homopolymer indels = 38.85% >>>>>>> Coverage mean coverageData = 4.5577X std coverageData = 323.0007X There is a 5.48% of reference with a coverageData >= 1X There is a 3.31% of reference with a coverageData >= 2X There is a 2.45% of reference with a coverageData >= 3X There is a 2.05% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 1.5% of reference with a coverageData >= 7X There is a 1.4% of reference with a coverageData >= 8X There is a 1.33% of reference with a coverageData >= 9X There is a 1.26% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1.16% of reference with a coverageData >= 12X There is a 1.12% of reference with a coverageData >= 13X There is a 1.08% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 1.02% of reference with a coverageData >= 16X There is a 0.99% of reference with a coverageData >= 17X There is a 0.97% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.92% of reference with a coverageData >= 20X There is a 0.9% of reference with a coverageData >= 21X There is a 0.88% of reference with a coverageData >= 22X There is a 0.86% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.83% of reference with a coverageData >= 25X There is a 0.82% of reference with a coverageData >= 26X There is a 0.8% of reference with a coverageData >= 27X There is a 0.79% of reference with a coverageData >= 28X There is a 0.78% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.74% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.71% of reference with a coverageData >= 35X There is a 0.7% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.68% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.66% of reference with a coverageData >= 41X There is a 0.65% of reference with a coverageData >= 42X There is a 0.65% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.63% of reference with a coverageData >= 46X There is a 0.62% of reference with a coverageData >= 47X There is a 0.61% of reference with a coverageData >= 48X There is a 0.61% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 721819580 2.89595900344818 131.11107383880884 chr2 243199373 1320237122 5.428620582833493 323.69877822082776 chr3 198022430 985963037 4.979047257424323 113.96991355796149 chr4 191154276 1508815347 7.893181249055606 918.0545151366816 chr5 180915260 1488332240 8.226681596676809 587.9965401197312 chr6 171115067 495343045 2.8947950270212033 94.01565718728493 chr7 159138663 685285750 4.306217842234856 129.45280989195712 chr8 146364022 424806863 2.9023994913176137 100.38330281008264 chr9 141213431 286433255 2.028371189423193 84.21504934845845 chr10 135534747 753076931 5.55633848639567 151.563339757097 chr11 135006516 1117917599 8.280471432949208 412.38055129073047 chr12 133851895 613627206 4.584374438628605 151.36021488735437 chr13 115169878 231427309 2.0094430333598163 81.59905088279918 chr14 107349540 231926072 2.1604756946326926 85.0734143200739 chr15 102531392 909181334 8.867346051441494 282.8704945765699 chr16 90354753 432936508 4.791518914339791 208.45956689138822 chr17 81195210 210838358 2.596684681276149 92.88073672640954 chr18 78077248 274469335 3.515356163680359 131.22115060993784 chr19 59128983 326110159 5.515233688358888 247.7653126699571 chr20 63025520 202548043 3.2137464792039796 144.00863550370755 chr21 48129895 200452234 4.1648176045262515 267.2407597357621 chr22 51304566 244752714 4.770583460349319 209.2805503937035 chrMT 16571 2374464 143.29032647396053 323.14309230751775 chrX 155270560 256685828 1.6531519432917612 135.44890898255562 chrY 59373566 183907219 3.0974595495914796 182.30852319469474