BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231835.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 = 2,539,723 number of mapped reads = 1,818,805 (71.61%) number of supplementary alignments = 15,571 (0.61%) number of secondary alignments = 0 number of mapped bases = 111,595,441 bp number of sequenced bases = 111,547,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 471,929 duplication rate = 18.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0975 >>>>>>> ACTG content number of A's = 28,031,193 bp (25.13%) number of C's = 19,551,702 bp (17.53%) number of T's = 37,286,105 bp (33.43%) number of G's = 26,639,476 bp (23.88%) number of N's = 39,189 bp (0.04%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 781,685 number of insertions = 7,224 mapped reads with insertion percentage = 0.39% number of deletions = 27,653 mapped reads with deletion percentage = 1.51% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.5393X There is a 1.78% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 9407405 0.037742754510529386 0.8222805444742237 chr2 243199373 8650563 0.0355698408811276 1.0017946328758052 chr3 198022430 7174742 0.036231966247459946 0.34711364937810296 chr4 191154276 6918481 0.03619317937726907 0.35805607849897697 chr5 180915260 6712733 0.03710429402141091 0.35312725576175935 chr6 171115067 6474770 0.037838690148775736 0.5073566863838348 chr7 159138663 7886196 0.04955549991016325 0.6629590700128881 chr8 146364022 5977781 0.04084187437811732 0.469687708262761 chr9 141213431 4485835 0.031766348060759175 0.36842271619216016 chr10 135534747 4979107 0.036736756516024635 0.4334490470976035 chr11 135006516 4808025 0.0356132810656339 0.37783645178641156 chr12 133851895 4689165 0.03503248870701457 0.34926833457475076 chr13 115169878 3462432 0.030063694258667183 0.3591828960144625 chr14 107349540 3510961 0.032705878385692194 0.33816567263862857 chr15 102531392 3517521 0.03430677113990611 0.3583831141340948 chr16 90354753 3565830 0.039464775029599164 0.3857296307387077 chr17 81195210 2900690 0.035724890667811565 0.3759724653007177 chr18 78077248 3058312 0.039170335511825416 0.8817856007355758 chr19 59128983 2117059 0.03580408274568159 0.5627965645414108 chr20 63025520 2249155 0.0356864171846579 0.35952099804911747 chr21 48129895 1585095 0.03293368913437272 0.3359722425395561 chr22 51304566 1078887 0.021029063962844943 0.268541817857386 chrMT 16571 191930 11.582282300404321 10.385242111768209 chrX 155270560 5357368 0.034503437097154796 0.35877069796186417 chrY 59373566 835398 0.014070200870198701 0.2712098423090915