BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240060.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 = 2,547,820 number of mapped reads = 2,046,461 (80.32%) number of supplementary alignments = 18,223 (0.72%) number of secondary alignments = 0 number of mapped bases = 136,127,826 bp number of sequenced bases = 136,059,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,150 duplication rate = 11.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9232 >>>>>>> ACTG content number of A's = 38,402,478 bp (28.22%) number of C's = 25,348,402 bp (18.63%) number of T's = 43,330,699 bp (31.85%) number of G's = 28,966,059 bp (21.29%) number of N's = 12,326 bp (0.01%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,157,565 number of insertions = 10,109 mapped reads with insertion percentage = 0.49% number of deletions = 38,484 mapped reads with deletion percentage = 1.86% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.5274X There is a 1.69% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 10827235 0.043439149545789896 0.7802594531033344 chr2 243199373 14891014 0.06122965621297058 0.6065277442709942 chr3 198022430 8618783 0.0435242765175642 0.4361932412838148 chr4 191154276 9195916 0.04810729946736844 0.46883539639317157 chr5 180915260 7062151 0.03903568444143407 0.4076159146595054 chr6 171115067 6894440 0.04029125033156782 0.44968911171731824 chr7 159138663 8102582 0.050915232334206556 0.7003638726183339 chr8 146364022 7707656 0.052660864976776876 0.6915924675775804 chr9 141213431 4846319 0.034319108074075476 0.4336753711282997 chr10 135534747 6566612 0.048449656972466254 0.5134401087450331 chr11 135006516 5815703 0.04307720228851769 0.505187585032103 chr12 133851895 6749267 0.05042339520109147 0.4683924678635072 chr13 115169878 3429881 0.02978105959268273 0.360653379534453 chr14 107349540 4648023 0.043298024379051836 0.44387829413413216 chr15 102531392 3860422 0.03765112249719579 0.4085704409151234 chr16 90354753 4027439 0.04457362635920215 0.435393595960086 chr17 81195210 3161005 0.038930929546213376 0.4145594732628577 chr18 78077248 3193335 0.040899686935687074 0.6585835435115538 chr19 59128983 2455465 0.04152726590951175 0.583483688615736 chr20 63025520 2712475 0.04303772503582676 0.4302638443750255 chr21 48129895 2379415 0.04943736112451523 0.4759100840639973 chr22 51304566 1168557 0.02277686161500713 0.29516864720714375 chrMT 16571 24119 1.4554945386518616 2.688930208034839 chrX 155270560 7446371 0.04795739127881036 0.47123618681451285 chrY 59373566 343641 0.005787777678706379 0.1399153676193048