BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230341.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 = 3,714,254 number of mapped reads = 2,862,519 (77.07%) number of supplementary alignments = 12,325 (0.33%) number of secondary alignments = 0 number of mapped bases = 174,805,774 bp number of sequenced bases = 174,697,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 303,110 duplication rate = 7.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.788 >>>>>>> ACTG content number of A's = 43,376,176 bp (24.83%) number of C's = 29,020,705 bp (16.61%) number of T's = 58,124,647 bp (33.27%) number of G's = 43,876,176 bp (25.12%) number of N's = 300,095 bp (0.17%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,817,325 number of insertions = 15,181 mapped reads with insertion percentage = 0.53% number of deletions = 66,416 mapped reads with deletion percentage = 2.29% homopolymer indels = 49.99% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.5465X There is a 4.06% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.31% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 17072101 0.06849371500663182 0.9610108929474622 chr2 243199373 14698218 0.06043690745863888 0.6019153224674177 chr3 198022430 11127675 0.05619401297115685 0.32588248478545695 chr4 191154276 11111789 0.058129952583430566 0.35890387563039494 chr5 180915260 12930800 0.07147434660846189 0.3770235089265017 chr6 171115067 9598572 0.05609425381576714 0.45321451712128197 chr7 159138663 10909213 0.06855161903678932 0.9965646134914784 chr8 146364022 9122443 0.06232708609223652 0.4468342284797992 chr9 141213431 7388370 0.052320589816984196 0.515255476140219 chr10 135534747 7466338 0.05508799894686785 0.45676867385602193 chr11 135006516 7471140 0.055339106743558956 0.5780741235163986 chr12 133851895 7788280 0.05818580304746526 0.33590755500448677 chr13 115169878 4528659 0.03932155767326592 0.27079395549636204 chr14 107349540 4567968 0.042552282944109496 0.31741247383371995 chr15 102531392 4898873 0.04777924989060911 0.32244572039556035 chr16 90354753 4500398 0.04980809365944479 0.3294219042630941 chr17 81195210 5035013 0.06201120731136726 0.4164941787164939 chr18 78077248 3606416 0.04619035752899488 0.7744358724399407 chr19 59128983 3302061 0.05584504979563068 0.6770707822392918 chr20 63025520 3519354 0.05584014221540735 0.3514456884833962 chr21 48129895 2110966 0.043859767406515225 0.30230736686524334 chr22 51304566 1917055 0.03736616736997639 0.2646391354974911 chrMT 16571 394614 23.813529660249834 18.90710308085176 chrX 155270560 9264523 0.05966696455528981 0.4068848635521431 chrY 59373566 474935 0.007999098454015715 0.16634451641206358