BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238494.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 = 2,432,750 number of mapped reads = 1,855,558 (76.27%) number of supplementary alignments = 16,567 (0.68%) number of secondary alignments = 0 number of mapped bases = 111,670,233 bp number of sequenced bases = 111,614,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 913,899 duplication rate = 22.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5131 >>>>>>> ACTG content number of A's = 27,574,366 bp (24.7%) number of C's = 19,013,656 bp (17.04%) number of T's = 38,623,091 bp (34.6%) number of G's = 26,401,246 bp (23.65%) number of N's = 2,303 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 811,858 number of insertions = 9,139 mapped reads with insertion percentage = 0.49% number of deletions = 33,657 mapped reads with deletion percentage = 1.79% homopolymer indels = 40.22% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 1.3028X There is a 0.75% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 3953035 0.015859679643486224 0.4559720632521789 chr2 243199373 8802834 0.03619595680454324 2.3832758472853635 chr3 198022430 3141337 0.015863541317011412 0.470433772074783 chr4 191154276 4678597 0.024475502708607995 0.5797517241049274 chr5 180915260 2554843 0.014121766179370386 0.4250936775145502 chr6 171115067 3509015 0.020506756427240858 0.9238983477353887 chr7 159138663 3559297 0.022366010452155177 0.7312369808934097 chr8 146364022 2680238 0.018312136844668016 1.2538548678839638 chr9 141213431 2690500 0.019052720275594747 0.8401849490653949 chr10 135534747 7181356 0.05298534994867405 0.857211251216399 chr11 135006516 2116074 0.015673865696971247 0.5119479199854932 chr12 133851895 2412815 0.018026005533952283 0.5011283912033475 chr13 115169878 2157165 0.018730288140098576 0.8199763008262856 chr14 107349540 1199189 0.011170881589245748 0.4786276570861197 chr15 102531392 1806564 0.017619618389653775 0.6016415709227084 chr16 90354753 1601763 0.017727490218472513 0.5665019840512667 chr17 81195210 1641137 0.020212239121002337 0.5170258980256036 chr18 78077248 8023780 0.10276719794222255 5.04101684565349 chr19 59128983 896052 0.015154192657093392 0.5567289444358605 chr20 63025520 28609666 0.4539378017031831 2.6730513138284864 chr21 48129895 14358708 0.29833241896746293 2.1413061809513994 chr22 51304566 410996 0.008010904916338246 0.277695113833899 chrMT 16571 21924 1.3230342164021482 3.693000161193583 chrX 155270560 3245949 0.020905115560863566 0.5820404060782726 chrY 59373566 417399 0.007030047681488425 0.5075032001923518