BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240053.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 = 1,669,027 number of mapped reads = 1,299,254 (77.84%) number of supplementary alignments = 5,453 (0.33%) number of secondary alignments = 0 number of mapped bases = 79,623,013 bp number of sequenced bases = 79,576,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,552 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2598 >>>>>>> ACTG content number of A's = 21,572,560 bp (27.11%) number of C's = 13,639,920 bp (17.14%) number of T's = 25,065,729 bp (31.5%) number of G's = 19,249,391 bp (24.19%) number of N's = 48,750 bp (0.06%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 862,840 number of insertions = 5,907 mapped reads with insertion percentage = 0.45% number of deletions = 26,883 mapped reads with deletion percentage = 2.05% homopolymer indels = 48.92% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2838X There is a 2.23% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5855508 0.023492450997744958 0.40557002009449455 chr2 243199373 7640199 0.03141537293354782 0.36328631089402125 chr3 198022430 5632243 0.028442449676029123 0.19296952059576308 chr4 191154276 5253758 0.02748438648581421 0.19730550092390917 chr5 180915260 4299557 0.02376558505899392 0.17723248184021523 chr6 171115067 4634545 0.027084377087612046 0.23350952799241342 chr7 159138663 4775026 0.03000544248634287 0.5438614833926366 chr8 146364022 4711242 0.032188525128121995 0.3659915341268762 chr9 141213431 2910791 0.020612706449997662 0.2719661271596858 chr10 135534747 3623789 0.0267369739510415 0.2242400410591689 chr11 135006516 3710731 0.0274855696594674 0.2655418661986924 chr12 133851895 3735997 0.027911424040728 0.19177704109320576 chr13 115169878 1763748 0.015314316821625876 0.13908105430109322 chr14 107349540 2850260 0.0265512083237618 0.1968296766196404 chr15 102531392 1946191 0.018981415955027704 0.19115422719909328 chr16 90354753 2328055 0.02576571705087833 0.190173534256241 chr17 81195210 2091800 0.025762603483629146 0.20075597894759262 chr18 78077248 1972106 0.025258395377869877 0.39777179019211145 chr19 59128983 1547820 0.02617701035040633 0.30836954051858473 chr20 63025520 1664311 0.026406938014950136 0.19480345213206307 chr21 48129895 1409015 0.029275256054475084 0.1997855030623101 chr22 51304566 717153 0.013978346488692645 0.13122191868535624 chrMT 16571 31649 1.9099028423148874 2.3096022040455355 chrX 155270560 4324575 0.027851867089292395 0.22150935706250893 chrY 59373566 192944 0.0032496616423544444 0.0703637365947509