BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472508.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,579,926 number of mapped reads = 18,290,719 (98.44%) number of supplementary alignments = 65,954 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,186,718 number of mapped paired reads (second in pair) = 9,104,001 number of mapped paired reads (both in pair) = 18,144,360 number of mapped paired reads (singletons) = 146,359 number of mapped bases = 1,799,148,533 bp number of sequenced bases = 1,798,894,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,962,368 duplication rate = 47.05% >>>>>>> Insert size mean insert size = 26,566.5539 std insert size = 1,579,222.4307 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 55.0314 >>>>>>> ACTG content number of A's = 500,999,619 bp (27.85%) number of C's = 401,466,854 bp (22.32%) number of T's = 497,537,318 bp (27.66%) number of G's = 398,612,065 bp (22.16%) number of N's = 278,621 bp (0.02%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 11,334,532 number of insertions = 95,812 mapped reads with insertion percentage = 0.52% number of deletions = 95,811 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.5812X std coverageData = 21.5375X There is a 5.37% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 157853798 0.6333135595277012 18.018624804575108 chr2 243199373 140613052 0.5781801583838787 20.56529916323894 chr3 198022430 254629098 1.2858598796106078 40.53925850838382 chr4 191154276 76056586 0.39788064170743426 16.09271078170526 chr5 180915260 98776762 0.5459835836954826 17.54987462529601 chr6 171115067 135704337 0.7930589595596512 23.802369592866253 chr7 159138663 71052834 0.4464837938219953 13.707701752799883 chr8 146364022 92617159 0.6327863756026054 24.39299475904767 chr9 141213431 111497575 0.7895677784360328 23.849096596120148 chr10 135534747 42379987 0.31268724764727673 12.06548015169304 chr11 135006516 84640749 0.6269382508915348 25.267446044179575 chr12 133851895 102886004 0.768655565167755 29.303735281774063 chr13 115169878 52386346 0.4548615220379065 29.36507928580495 chr14 107349540 31660377 0.2949279242370298 11.98322099054497 chr15 102531392 37561616 0.3663425929104718 12.12209544237111 chr16 90354753 53175107 0.5885147735393621 19.326905391030344 chr17 81195210 60187825 0.7412730997308832 22.07364512920394 chr18 78077248 23745632 0.3041299816305001 11.48589804778213 chr19 59128983 29466905 0.49834959955255786 12.275122756919961 chr20 63025520 40121638 0.6365935259241019 23.190825442093878 chr21 48129895 9249973 0.19218768293593827 9.779473748143522 chr22 51304566 17236136 0.335957154378813 11.909213251368667 chrMT 16571 7906 0.47709854565204274 1.141490256525626 chrX 155270560 72754923 0.4685686906777434 15.630353303536996 chrY 59373566 2886208 0.04861099297960308 1.8605339793433224