BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013368.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 = 2,598,597 number of mapped reads = 2,309,879 (88.89%) number of supplementary alignments = 15,231 (0.59%) number of secondary alignments = 0 number of mapped bases = 153,574,589 bp number of sequenced bases = 153,513,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,259 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8717 >>>>>>> ACTG content number of A's = 42,398,463 bp (27.62%) number of C's = 28,399,478 bp (18.5%) number of T's = 48,276,729 bp (31.45%) number of G's = 34,408,046 bp (22.41%) number of N's = 31,110 bp (0.02%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,257,440 number of insertions = 11,158 mapped reads with insertion percentage = 0.48% number of deletions = 35,693 mapped reads with deletion percentage = 1.53% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 0.0496X std coverageData = 0.6035X There is a 4.23% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10591416 0.04249303755997463 1.0076297413019064 chr2 243199373 18002702 0.07402445893641346 0.7137447534744177 chr3 198022430 10613350 0.053596706191313785 0.2596355890222415 chr4 191154276 12944462 0.06771735516918283 0.3208292918807223 chr5 180915260 5690046 0.03145144306787609 0.2038941389680924 chr6 171115067 7332996 0.04285418069000318 0.38797804581163525 chr7 159138663 10633812 0.06682104649829815 1.387510459176866 chr8 146364022 11169070 0.07631021508824075 0.7171839168026617 chr9 141213431 4970911 0.03520140375315999 0.49594928243040054 chr10 135534747 5513761 0.040681530913987685 0.5831823669880452 chr11 135006516 6528897 0.04835986583047592 0.42211583925537327 chr12 133851895 6837555 0.05108298989715461 0.2697796980666681 chr13 115169878 4021413 0.03491722896502504 0.2107886659813085 chr14 107349540 6723968 0.06263620691807342 0.31541935803405824 chr15 102531392 2683187 0.02616941941059378 0.18892509474879618 chr16 90354753 4227172 0.046784168620327034 0.2985157772317586 chr17 81195210 4812582 0.05927174768068215 0.3127684453620905 chr18 78077248 3855667 0.04938272158362959 1.0875187607019114 chr19 59128983 1820592 0.03079017949623791 0.7344547529302367 chr20 63025520 3048262 0.048365519237286735 0.27299331812576194 chr21 48129895 2972708 0.06176427353519055 0.2940191474424403 chr22 51304566 1597143 0.03113062100554559 0.19601792825785924 chrMT 16571 175251 10.575764890471305 6.610345762712962 chrX 155270560 6510700 0.04193132297584294 0.2912852821090614 chrY 59373566 296966 0.005001653429406615 0.11903328559317354