BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234098.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 = 4,484,057 number of mapped reads = 4,177,165 (93.16%) number of supplementary alignments = 33,182 (0.74%) number of secondary alignments = 0 number of mapped bases = 266,406,460 bp number of sequenced bases = 266,300,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 679,984 duplication rate = 13.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.5233 >>>>>>> ACTG content number of A's = 66,099,223 bp (24.82%) number of C's = 49,577,358 bp (18.62%) number of T's = 85,834,119 bp (32.23%) number of G's = 64,764,288 bp (24.32%) number of N's = 25,682 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,424,844 number of insertions = 16,632 mapped reads with insertion percentage = 0.39% number of deletions = 60,982 mapped reads with deletion percentage = 1.45% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0861X std coverageData = 0.806X There is a 5.34% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 60713534 0.2435842837880031 0.9091517565195838 chr2 243199373 18871975 0.07759878147383217 1.8694313530736055 chr3 198022430 30549250 0.15427166508359685 0.570745180993647 chr4 191154276 7500730 0.039239143151576686 0.3047414321879649 chr5 180915260 2081520 0.011505497104003278 0.17805894108024273 chr6 171115067 4225973 0.024696673846961704 0.5849320070525591 chr7 159138663 9962099 0.06260011748370664 0.5094522696783909 chr8 146364022 5186762 0.035437410977951944 0.64633774765962 chr9 141213431 1865220 0.013208516971731959 0.37691993641831684 chr10 135534747 12676238 0.09352758816895862 0.5839239020697258 chr11 135006516 20878765 0.15465005407590846 1.0383336767822133 chr12 133851895 1658644 0.012391636293232904 0.18207539565493458 chr13 115169878 8816886 0.07655548614890431 0.4895609011564624 chr14 107349540 16517224 0.1538639476238091 0.618307025037386 chr15 102531392 1070858 0.010444196446684349 0.2547699786911455 chr16 90354753 12575976 0.13918444334632846 0.6160863560073909 chr17 81195210 4353139 0.053613248860369965 0.48795431438842457 chr18 78077248 1334441 0.017091291434862047 1.5527399966052597 chr19 59128983 16660159 0.28175960679046347 1.0380853551366651 chr20 63025520 18001715 0.2856258068160326 0.8449455987689999 chr21 48129895 7666762 0.15929313787200242 0.6066386150873885 chr22 51304566 505573 0.009854347077022345 0.13325944308451154 chrMT 16571 164284 9.913946050328887 6.102003341135347 chrX 155270560 2155339 0.013881182627279762 0.358401718100653 chrY 59373566 413394 0.006962593420782575 0.23045642700385868