BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068152.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 = 3,132,915 number of mapped reads = 2,896,757 (92.46%) number of supplementary alignments = 24,614 (0.79%) number of secondary alignments = 0 number of mapped bases = 183,170,951 bp number of sequenced bases = 183,097,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 721,041 duplication rate = 17.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.495 >>>>>>> ACTG content number of A's = 46,587,356 bp (25.44%) number of C's = 32,885,606 bp (17.96%) number of T's = 59,889,992 bp (32.71%) number of G's = 43,714,507 bp (23.88%) number of N's = 19,897 bp (0.01%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,129,637 number of insertions = 11,762 mapped reads with insertion percentage = 0.4% number of deletions = 42,538 mapped reads with deletion percentage = 1.46% homopolymer indels = 44.15% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.711X There is a 3.04% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 15411753 0.06183235547485356 1.04213510639389 chr2 243199373 13234206 0.05441710575462709 1.5251969651692139 chr3 198022430 11619787 0.0586791455897193 0.4376212232882163 chr4 191154276 13522877 0.07074326184573554 0.47476346266441427 chr5 180915260 14417596 0.07969253671580827 0.4927936423415924 chr6 171115067 16936083 0.0989748202593989 0.7322459282181377 chr7 159138663 7744437 0.0486647107246339 0.5483952073010446 chr8 146364022 7981778 0.05453374327196338 0.742705217409977 chr9 141213431 5947392 0.04211633382096636 0.4618929203384132 chr10 135534747 13260949 0.09784169221196097 0.6322959044373148 chr11 135006516 7315469 0.05418604387954134 0.49024631643853334 chr12 133851895 7454580 0.05569274906418023 0.4231303134458191 chr13 115169878 5325257 0.04623827942233298 0.42412974569423045 chr14 107349540 5199767 0.048437720366570736 0.40917115918380065 chr15 102531392 5652179 0.055126326579083215 0.4565042293259618 chr16 90354753 4553941 0.050400680083758295 0.41872595589054984 chr17 81195210 6638671 0.08176185516362357 0.5322671508448776 chr18 78077248 4008390 0.051338771571457026 0.8173348300085835 chr19 59128983 3569892 0.06037465586039253 0.7613880046045671 chr20 63025520 2732651 0.04335784932833557 0.40173399438072543 chr21 48129895 1936983 0.04024490392094145 0.3726868059358402 chr22 51304566 1451958 0.028300755921022703 0.30357235312109504 chrMT 16571 295577 17.837004405286343 13.778215354202837 chrX 155270560 6196265 0.039906244944308826 0.3845753154681622 chrY 59373566 762513 0.012842634380424447 0.23644301628415698