BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240223.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 = 2,158,536 number of mapped reads = 1,764,848 (81.76%) number of supplementary alignments = 16,677 (0.77%) number of secondary alignments = 0 number of mapped bases = 119,350,340 bp number of sequenced bases = 119,301,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,525 duplication rate = 8.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9871 >>>>>>> ACTG content number of A's = 34,125,576 bp (28.6%) number of C's = 22,471,907 bp (18.84%) number of T's = 37,673,950 bp (31.58%) number of G's = 25,018,772 bp (20.97%) number of N's = 10,822 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 916,005 number of insertions = 9,248 mapped reads with insertion percentage = 0.52% number of deletions = 27,606 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.4867X There is a 1.83% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.25% 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 10282862 0.04125511085486924 0.7634810281723715 chr2 243199373 8785528 0.0361247970816109 0.4764498201114253 chr3 198022430 8057715 0.04069092072044566 0.3749649075934364 chr4 191154276 8033131 0.04202433326681115 0.38801090761882134 chr5 180915260 7920310 0.043779115150374824 0.382547889375558 chr6 171115067 7562337 0.044194454249899574 0.4344710453680723 chr7 159138663 6595750 0.04144655909293394 0.4677530871667658 chr8 146364022 5866294 0.04008016396269843 0.7208364069803173 chr9 141213431 6418286 0.045450959972780494 0.5103371641803482 chr10 135534747 4441997 0.0327738613036257 0.4158391503464178 chr11 135006516 6103585 0.045209558626044394 0.5282224397734061 chr12 133851895 4468340 0.03338271751774601 0.33759416996151054 chr13 115169878 3460613 0.03004790019834874 0.3209927557037572 chr14 107349540 3933078 0.03663805173268558 0.37884842245466765 chr15 102531392 3039138 0.02964104886043096 0.3265930422232423 chr16 90354753 3523044 0.038991241556490114 0.3807940723163331 chr17 81195210 2377447 0.029280631209648942 0.34237255732824606 chr18 78077248 3623406 0.04640796253474508 0.9047446511884362 chr19 59128983 2286075 0.03866251174994841 0.5867397264359789 chr20 63025520 2176123 0.03452764848270986 0.3554413269131983 chr21 48129895 2050130 0.04259577129765191 0.4135261271591125 chr22 51304566 1146884 0.0223544235809343 0.2605577017750456 chrMT 16571 8265 0.4987628990404924 1.185542539156465 chrX 155270560 6858138 0.044168952568986675 0.41650062671607707 chrY 59373566 331864 0.005589423414453496 0.1575115946503393