BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008830.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 = 2,215,324 number of mapped reads = 1,921,638 (86.74%) number of supplementary alignments = 11,741 (0.53%) number of secondary alignments = 0 number of mapped bases = 126,076,237 bp number of sequenced bases = 126,004,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,597 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7667 >>>>>>> ACTG content number of A's = 35,039,476 bp (27.81%) number of C's = 24,260,936 bp (19.25%) number of T's = 38,580,860 bp (30.62%) number of G's = 27,950,204 bp (22.18%) number of N's = 173,028 bp (0.14%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,101,226 number of insertions = 9,508 mapped reads with insertion percentage = 0.49% number of deletions = 40,322 mapped reads with deletion percentage = 2.07% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3964X There is a 3.37% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 10604715 0.04254639349524429 0.7326106015839909 chr2 243199373 10131879 0.04166079408436633 0.4701107185165055 chr3 198022430 8664767 0.04375649263570799 0.2600111572390007 chr4 191154276 8571619 0.04484136677120422 0.27798812423381547 chr5 180915260 9768735 0.05399619136605724 0.2725849478467879 chr6 171115067 8237193 0.048138326708541686 0.2896309386323064 chr7 159138663 6832887 0.04293668723357315 0.3789375028917154 chr8 146364022 6476086 0.044246433730824916 0.5372256140486205 chr9 141213431 5627604 0.03985176169255458 0.34594941165029797 chr10 135534747 5706130 0.04210086436358641 0.6117271162682149 chr11 135006516 5050014 0.03740570566238447 0.29348378910633305 chr12 133851895 5639987 0.04213602653888464 0.24239749217741682 chr13 115169878 3675797 0.03191630540756499 0.20548699898674774 chr14 107349540 3326054 0.03098340244401606 0.23261594324355972 chr15 102531392 3404968 0.033209029289293174 0.21081720660776207 chr16 90354753 2867233 0.03173306223304047 0.26621722433693645 chr17 81195210 4069298 0.05011746382576016 0.27938802007439695 chr18 78077248 3051735 0.039086098423960845 0.5801293491079322 chr19 59128983 2877976 0.048672847966960635 0.5114393603128814 chr20 63025520 2941940 0.04667855179933462 0.2631767205370182 chr21 48129895 1592556 0.03308870713306148 0.2502979624555937 chr22 51304566 1386601 0.027026853711227185 0.18887688481309856 chrMT 16571 11809 0.7126304990646309 0.9449929987564264 chrX 155270560 5181810 0.03337277845845343 0.23516654121881192 chrY 59373566 376844 0.006346999605851534 0.2212778064656051