BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013216.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 = 1,518,738 number of mapped reads = 1,301,594 (85.7%) number of supplementary alignments = 11,888 (0.78%) number of secondary alignments = 0 number of mapped bases = 83,839,846 bp number of sequenced bases = 83,794,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,339 duplication rate = 9.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4144 >>>>>>> ACTG content number of A's = 22,898,756 bp (27.33%) number of C's = 15,180,124 bp (18.12%) number of T's = 26,935,194 bp (32.14%) number of G's = 18,771,413 bp (22.4%) number of N's = 9,076 bp (0.01%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 663,506 number of insertions = 6,038 mapped reads with insertion percentage = 0.46% number of deletions = 25,049 mapped reads with deletion percentage = 1.9% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.3053X There is a 1.54% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 5809576 0.023308170614347236 0.3731065000940559 chr2 243199373 7553023 0.03105691806203793 0.37659667307424255 chr3 198022430 6579777 0.03322743287212464 0.28599843213896925 chr4 191154276 4971800 0.0260093580119547 0.26370483743584117 chr5 180915260 4967020 0.027454953219534936 0.26645173117945475 chr6 171115067 4685357 0.027381323469312026 0.286686694523351 chr7 159138663 4913357 0.030874690709196167 0.37466485710185493 chr8 146364022 4573037 0.031244269852054217 0.34881739089507247 chr9 141213431 3186793 0.02256720892221647 0.2701431982711763 chr10 135534747 3832781 0.028278954916262176 0.30820497406318936 chr11 135006516 3726953 0.02760572682284461 0.29598564743111244 chr12 133851895 3764197 0.028122104659033777 0.2751609741182175 chr13 115169878 2280497 0.01980115842442761 0.23231715570267383 chr14 107349540 2666728 0.024841541007069055 0.257372694733358 chr15 102531392 2393091 0.023340081055370828 0.24309465471453387 chr16 90354753 2372007 0.02625215521312974 0.26047835476491205 chr17 81195210 1881620 0.02317402713780776 0.25037550931074654 chr18 78077248 2328062 0.029817418769677948 0.39964615589220503 chr19 59128983 1571134 0.026571300913462353 0.3186664125049987 chr20 63025520 1964283 0.031166470344076495 0.2842226741599876 chr21 48129895 1182204 0.02456277953650221 0.26005864452968336 chr22 51304566 828269 0.016144157617472097 0.19846453505446005 chrMT 16571 162897 9.830245609800253 11.392851884180397 chrX 155270560 5459471 0.03516101828962297 0.2999844146689362 chrY 59373566 185912 0.00313122509771436 0.08730576156005979