BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524597.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,046,447 number of mapped reads = 2,828,002 (92.83%) number of supplementary alignments = 5,886 (0.19%) number of secondary alignments = 0 number of mapped bases = 164,172,325 bp number of sequenced bases = 164,124,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,662 duplication rate = 5.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3892 >>>>>>> ACTG content number of A's = 39,139,937 bp (23.85%) number of C's = 30,147,178 bp (18.37%) number of T's = 53,170,608 bp (32.4%) number of G's = 41,665,415 bp (25.39%) number of N's = 1,009 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 749,132 number of insertions = 10,102 mapped reads with insertion percentage = 0.36% number of deletions = 28,177 mapped reads with deletion percentage = 0.99% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.4368X There is a 4.29% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16650555 0.06680246144702684 0.8022776003548837 chr2 243199373 14546056 0.05981123972716821 0.527923336522715 chr3 198022430 11703902 0.0591039207023164 0.2944094391281137 chr4 191154276 7328870 0.038340078774905355 0.2865035603385091 chr5 180915260 10035901 0.05547293799317979 0.28354351448738274 chr6 171115067 10477547 0.06123100194327131 0.3339541800967624 chr7 159138663 9934365 0.06242584179559181 0.6051243477903757 chr8 146364022 14647240 0.10007404688564789 0.5615191094503836 chr9 141213431 5903044 0.04180228437336106 0.37824614976332505 chr10 135534747 7008759 0.05171189790910223 0.432094679355264 chr11 135006516 8336760 0.06175079727262942 0.4211216917097477 chr12 133851895 5418654 0.04048246011010901 0.2567812151234886 chr13 115169878 3974527 0.034510125989714084 0.22958612826925578 chr14 107349540 3040136 0.028319972307287018 0.21989899201027482 chr15 102531392 4155190 0.0405260273848618 0.2563428574055645 chr16 90354753 4812783 0.05326541039849891 0.30306976692937687 chr17 81195210 3582551 0.044122689010841896 0.26686081836828107 chr18 78077248 4372733 0.05600521422066516 0.6422327568137994 chr19 59128983 3208630 0.05426492791191758 0.5640732780625052 chr20 63025520 2982511 0.04732227516726558 0.2731658252578712 chr21 48129895 1430599 0.029723709141688343 0.2423243682457865 chr22 51304566 2653643 0.05172333004434732 0.27496436113174894 chrMT 16571 16891 1.019310844245972 1.1345405646134923 chrX 155270560 7552506 0.04864094004684468 0.3189604914231598 chrY 59373566 397972 0.006702848200156952 0.1826462425691989