BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234120.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 = 935,405 number of mapped reads = 689,345 (73.69%) number of supplementary alignments = 2,775 (0.3%) number of secondary alignments = 0 number of mapped bases = 45,669,203 bp number of sequenced bases = 45,646,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,304 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1193 >>>>>>> ACTG content number of A's = 13,160,888 bp (28.83%) number of C's = 7,862,577 bp (17.23%) number of T's = 14,539,267 bp (31.85%) number of G's = 10,075,369 bp (22.07%) number of N's = 8,022 bp (0.02%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 404,353 number of insertions = 3,779 mapped reads with insertion percentage = 0.54% number of deletions = 12,900 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1681X There is a 1.38% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5039792 0.02021977710538984 0.2652361187084331 chr2 243199373 2730104 0.011225785520425663 0.15810390354690013 chr3 198022430 5209649 0.026308378298357412 0.1710023763603537 chr4 191154276 2450964 0.012821915634259733 0.12106420043765513 chr5 180915260 2564475 0.01417500657490142 0.12462147464685186 chr6 171115067 2843823 0.016619360585003306 0.15075623657774292 chr7 159138663 3190910 0.02005112987533394 0.23249480983181614 chr8 146364022 2462826 0.016826717155941504 0.28708920851623815 chr9 141213431 1876556 0.01328879262199925 0.14036294429998772 chr10 135534747 1693185 0.012492626706271862 0.14710231686005223 chr11 135006516 1690175 0.012519210554252064 0.13173351740233616 chr12 133851895 1013756 0.0075737142159997065 0.09140019425880773 chr13 115169878 1169726 0.010156527212783885 0.1051510287916452 chr14 107349540 2370516 0.022082218517191596 0.16006039136730063 chr15 102531392 841586 0.008208081286948684 0.09482814757987144 chr16 90354753 815720 0.009027970006182186 0.10722698992099548 chr17 81195210 1019657 0.012558093020511925 0.1226560719086536 chr18 78077248 917080 0.01174580333569134 0.22742629346234194 chr19 59128983 1147045 0.01939903143607256 0.1877020493940886 chr20 63025520 1083372 0.017189417873902508 0.13863876490518529 chr21 48129895 783726 0.016283559313811095 0.1373173868469668 chr22 51304566 367551 0.0071640991953815574 0.08841656358071966 chrMT 16571 13152 0.7936756985094442 1.1018593442920448 chrX 155270560 2260305 0.014557202601703761 0.13002352541096318 chrY 59373566 113552 0.0019125009267592248 0.052953874803647126