BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237250.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 = 2,845,576 number of mapped reads = 1,635,213 (57.47%) number of supplementary alignments = 16,842 (0.59%) number of secondary alignments = 0 number of mapped bases = 101,957,072 bp number of sequenced bases = 101,902,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 439,241 duplication rate = 16.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2532 >>>>>>> ACTG content number of A's = 28,021,544 bp (27.5%) number of C's = 18,117,402 bp (17.78%) number of T's = 33,184,424 bp (32.56%) number of G's = 22,543,317 bp (22.12%) number of N's = 35,921 bp (0.04%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 893,089 number of insertions = 8,097 mapped reads with insertion percentage = 0.49% number of deletions = 32,177 mapped reads with deletion percentage = 1.94% homopolymer indels = 44.65% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.4885X There is a 1.11% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 11877804 0.04765405980673565 0.614487676594342 chr2 243199373 9856593 0.04052885860030568 0.6264972947176852 chr3 198022430 6430195 0.03247205379713803 0.4295926311702798 chr4 191154276 4475943 0.023415343321956345 0.4015967130562706 chr5 180915260 5493595 0.030365570046440526 0.40822226843155535 chr6 171115067 10252227 0.059914227190759305 0.7483322376709296 chr7 159138663 6835046 0.04295025401840909 0.5205762325430061 chr8 146364022 6183761 0.042249187440339675 0.5105008264710402 chr9 141213431 4646875 0.032906749500336126 0.46395125425496075 chr10 135534747 5742945 0.04237249212558017 0.548769819224809 chr11 135006516 3390022 0.025110062095076952 0.3748846323599821 chr12 133851895 2000583 0.014946243383405219 0.2798868427112951 chr13 115169878 3441935 0.029885722376123382 0.4355167008363801 chr14 107349540 2605691 0.024272959157533417 0.4250760191738732 chr15 102531392 1826385 0.017812934793667873 0.394047815594291 chr16 90354753 1497570 0.01657433560800061 0.29634528507156904 chr17 81195210 2134941 0.02629392792998503 0.3690795996039269 chr18 78077248 2607417 0.0333953496926531 0.5593077841254764 chr19 59128983 1149373 0.019438402990966375 0.36069380250073024 chr20 63025520 2211835 0.03509427609641301 0.43300431949342494 chr21 48129895 1006093 0.0209037023662736 0.33645308679267577 chr22 51304566 1045587 0.020379998926411347 0.34352104127759386 chrMT 16571 376458 22.717880634844004 16.4831746333253 chrX 155270560 4613054 0.029709778853119356 0.4178873590267492 chrY 59373566 255144 0.0042972658910195825 0.1632952170521381