BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231886.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 = 5,565,233 number of mapped reads = 5,214,472 (93.7%) number of supplementary alignments = 30,768 (0.55%) number of secondary alignments = 0 number of mapped bases = 353,221,877 bp number of sequenced bases = 353,092,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 506,515 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2146 >>>>>>> ACTG content number of A's = 93,466,337 bp (26.47%) number of C's = 64,952,258 bp (18.4%) number of T's = 101,939,414 bp (28.87%) number of G's = 92,657,116 bp (26.24%) number of N's = 77,849 bp (0.02%) GC percentage = 44.64% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,374,590 number of insertions = 25,498 mapped reads with insertion percentage = 0.48% number of deletions = 79,092 mapped reads with deletion percentage = 1.5% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 33.0495X There is a 7.8% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 23135446 0.09282001347551307 1.2115105462737183 chr2 243199373 38793420 0.15951282900717018 117.87356041888535 chr3 198022430 26551715 0.13408438124913424 0.48475174593842474 chr4 191154276 23220092 0.12147304515437572 0.523315772560149 chr5 180915260 18976347 0.10489080357289927 0.43981870213601876 chr6 171115067 25749856 0.15048269244461096 0.7123895849298458 chr7 159138663 21121509 0.13272393145592784 1.6917986628579453 chr8 146364022 15154615 0.1035405750191806 1.220867510704827 chr9 141213431 10552418 0.07472673049067124 0.894686676377713 chr10 135534747 13983240 0.10317088650337024 0.6129325974483986 chr11 135006516 16185773 0.11988882818070797 1.3382270487095778 chr12 133851895 10328194 0.07716135808163194 0.3742188270227399 chr13 115169878 18092305 0.15709233450781288 0.53745099171632 chr14 107349540 16001140 0.1490564375031323 0.6674076472116066 chr15 102531392 7714292 0.07523834261413324 0.3713250263705694 chr16 90354753 7403044 0.08193308878836733 0.5225597299151191 chr17 81195210 9719575 0.11970626099741598 0.745099195471372 chr18 78077248 10102444 0.1293903699064803 1.916584409219666 chr19 59128983 8366331 0.14149289528622536 0.8809236090185859 chr20 63025520 9962884 0.15807698214945312 0.5806709100975549 chr21 48129895 9405205 0.19541295487970625 0.6846274444427904 chr22 51304566 3471473 0.06766401649319088 0.33916721046348197 chrMT 16571 6098 0.36799227566230164 0.794418975630257 chrX 155270560 8417443 0.05421145515286349 0.5251388561055375 chrY 59373566 807018 0.013592210378605186 0.25726275915651114