BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004047.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 = 2,700,896 number of mapped reads = 2,458,617 (91.03%) number of supplementary alignments = 24,125 (0.89%) number of secondary alignments = 0 number of mapped bases = 161,252,367 bp number of sequenced bases = 161,182,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,624 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4371 >>>>>>> ACTG content number of A's = 44,631,876 bp (27.69%) number of C's = 30,405,292 bp (18.86%) number of T's = 50,110,934 bp (31.09%) number of G's = 36,015,520 bp (22.34%) number of N's = 19,324 bp (0.01%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,157,605 number of insertions = 10,866 mapped reads with insertion percentage = 0.44% number of deletions = 39,631 mapped reads with deletion percentage = 1.6% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0521X std coverageData = 0.3855X There is a 4.16% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 11328081 0.04544855677611331 0.6150280268227221 chr2 243199373 12547781 0.05159462726081946 0.4360635777492246 chr3 198022430 9178578 0.04635120374999943 0.2575018182857917 chr4 191154276 11516059 0.060244841187858125 0.31256033957976814 chr5 180915260 13647900 0.07543808078986813 0.3342162874412405 chr6 171115067 10892468 0.0636558088715823 0.33741257975477656 chr7 159138663 9032423 0.05675819332477363 0.6186246697364803 chr8 146364022 8858289 0.06052231196543642 0.45448578410828644 chr9 141213431 3519484 0.02492315337908616 0.264886937069636 chr10 135534747 7331857 0.054095773683777194 0.3592379816718713 chr11 135006516 5516445 0.04086058335139913 0.3545577598813223 chr12 133851895 9337948 0.06976328575699284 0.3202117719904103 chr13 115169878 7135444 0.061955817996090956 0.30109302995948556 chr14 107349540 4702811 0.0438083945212993 0.2559029857701829 chr15 102531392 5405108 0.05271661580484541 0.29068758850712173 chr16 90354753 4371729 0.04838405125184726 0.27667056393855827 chr17 81195210 2975892 0.03665107830868348 0.24577687496856634 chr18 78077248 4543155 0.0581879499646299 0.48260290186919746 chr19 59128983 2392456 0.04046164636384834 0.4681756232581018 chr20 63025520 3643274 0.05780632988034053 0.2948783391063334 chr21 48129895 1600454 0.033252804727706135 0.23311029856737184 chr22 51304566 1127964 0.021985645488161815 0.17503701077826023 chrMT 16571 20200 1.2189970430269748 1.4380083248339326 chrX 155270560 10243791 0.06597381370943725 0.3436839893565811 chrY 59373566 382776 0.006446909387251559 0.1263538043980821