BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472765.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 = 18,264,274 number of mapped reads = 18,102,937 (99.12%) number of supplementary alignments = 68,227 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,083,979 number of mapped paired reads (second in pair) = 9,018,958 number of mapped paired reads (both in pair) = 18,002,488 number of mapped paired reads (singletons) = 100,449 number of mapped bases = 1,786,239,131 bp number of sequenced bases = 1,785,974,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,475,774 duplication rate = 46.25% >>>>>>> Insert size mean insert size = 28,955.8792 std insert size = 1,675,540.7097 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.2271 >>>>>>> ACTG content number of A's = 490,254,157 bp (27.45%) number of C's = 405,976,206 bp (22.73%) number of T's = 487,107,647 bp (27.27%) number of G's = 402,292,299 bp (22.53%) number of N's = 344,610 bp (0.02%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 11,264,873 number of insertions = 106,167 mapped reads with insertion percentage = 0.58% number of deletions = 103,777 mapped reads with deletion percentage = 0.57% homopolymer indels = 44.97% >>>>>>> Coverage mean coverageData = 0.577X std coverageData = 21.6315X There is a 5.26% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 222892284 0.89424966367486 42.49881821173129 chr2 243199373 132973064 0.5467656530512519 28.06644975362118 chr3 198022430 198027918 1.0000277140321931 21.990647719763025 chr4 191154276 67099231 0.3510213446650809 12.596567336552948 chr5 180915260 109949260 0.6077390044377683 24.798729846530286 chr6 171115067 97641573 0.570619377427471 15.360115851894797 chr7 159138663 73975029 0.46484636483341574 13.531858660646659 chr8 146364022 64135345 0.4381906435995589 13.587322820335713 chr9 141213431 101912723 0.7216928466244829 18.34385320782479 chr10 135534747 40724936 0.300475980524758 9.868357959746943 chr11 135006516 77515357 0.5741601168346571 16.923666567169754 chr12 133851895 93667487 0.6997845417130628 19.27333494360028 chr13 115169878 34403485 0.298719470728275 11.392823717323092 chr14 107349540 44793376 0.4172665853994344 14.576007976160218 chr15 102531392 40047597 0.39058864040390673 12.123588570250204 chr16 90354753 62041316 0.6866414210661391 21.871643042355455 chr17 81195210 56756863 0.6990173804587734 15.01109823702615 chr18 78077248 30609785 0.39204487586447717 13.022662072531125 chr19 59128983 53310895 0.9016034488535005 31.648433654145368 chr20 63025520 50255079 0.7973766658331419 26.701446828747482 chr21 48129895 6165193 0.12809487741454662 3.732492136337846 chr22 51304566 16695190 0.3254133365049809 9.880742075799494 chrMT 16571 7686 0.46382234023293706 1.4784485923960402 chrX 155270560 105960463 0.6824246850143388 23.360729137781384 chrY 59373566 4677996 0.07878920393631064 5.005730002504406