BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352031.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,669,981,148 number of mapped reads = 1,621,574,852 (97.1%) number of supplementary alignments = 39,396,406 (2.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 811,735,421 number of mapped paired reads (second in pair) = 809,839,431 number of mapped paired reads (both in pair) = 1,607,370,294 number of mapped paired reads (singletons) = 14,204,558 number of mapped bases = 146,573,255,828 bp number of sequenced bases = 146,480,027,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 639,800,565 duplication rate = 35.95% >>>>>>> Insert size mean insert size = 155,716.4308 std insert size = 3,869,616.9676 median insert size = 276 >>>>>>> Mapping quality mean mapping quality = 52.9561 >>>>>>> ACTG content number of A's = 42,243,552,486 bp (28.84%) number of C's = 30,727,988,466 bp (20.98%) number of T's = 41,844,404,666 bp (28.57%) number of G's = 31,661,019,516 bp (21.61%) number of N's = 3,062,450 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,052,758,656 number of insertions = 18,956,685 mapped reads with insertion percentage = 1.15% number of deletions = 61,707,593 mapped reads with deletion percentage = 3.73% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 47.3475X std coverageData = 389.8482X There is a 91.81% of reference with a coverageData >= 1X There is a 91.74% of reference with a coverageData >= 2X There is a 91.7% of reference with a coverageData >= 3X There is a 91.67% of reference with a coverageData >= 4X There is a 91.64% of reference with a coverageData >= 5X There is a 91.62% of reference with a coverageData >= 6X There is a 91.6% of reference with a coverageData >= 7X There is a 91.57% of reference with a coverageData >= 8X There is a 91.55% of reference with a coverageData >= 9X There is a 91.53% of reference with a coverageData >= 10X There is a 91.5% of reference with a coverageData >= 11X There is a 91.47% of reference with a coverageData >= 12X There is a 91.44% of reference with a coverageData >= 13X There is a 91.4% of reference with a coverageData >= 14X There is a 91.35% of reference with a coverageData >= 15X There is a 91.3% of reference with a coverageData >= 16X There is a 91.23% of reference with a coverageData >= 17X There is a 91.15% of reference with a coverageData >= 18X There is a 91.04% of reference with a coverageData >= 19X There is a 90.91% of reference with a coverageData >= 20X There is a 90.74% of reference with a coverageData >= 21X There is a 90.52% of reference with a coverageData >= 22X There is a 90.24% of reference with a coverageData >= 23X There is a 89.88% of reference with a coverageData >= 24X There is a 89.44% of reference with a coverageData >= 25X There is a 88.9% of reference with a coverageData >= 26X There is a 88.23% of reference with a coverageData >= 27X There is a 87.43% of reference with a coverageData >= 28X There is a 86.48% of reference with a coverageData >= 29X There is a 85.38% of reference with a coverageData >= 30X There is a 84.1% of reference with a coverageData >= 31X There is a 82.66% of reference with a coverageData >= 32X There is a 81.05% of reference with a coverageData >= 33X There is a 79.27% of reference with a coverageData >= 34X There is a 77.32% of reference with a coverageData >= 35X There is a 75.23% of reference with a coverageData >= 36X There is a 73% of reference with a coverageData >= 37X There is a 70.64% of reference with a coverageData >= 38X There is a 68.19% of reference with a coverageData >= 39X There is a 65.65% of reference with a coverageData >= 40X There is a 63.06% of reference with a coverageData >= 41X There is a 60.42% of reference with a coverageData >= 42X There is a 57.76% of reference with a coverageData >= 43X There is a 55.09% of reference with a coverageData >= 44X There is a 52.44% of reference with a coverageData >= 45X There is a 49.82% of reference with a coverageData >= 46X There is a 47.24% of reference with a coverageData >= 47X There is a 44.72% of reference with a coverageData >= 48X There is a 42.26% of reference with a coverageData >= 49X There is a 39.87% of reference with a coverageData >= 50X There is a 37.56% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12393472880 49.722936818680985 880.3971722318139 chr2 243199373 12395471861 50.968354515453456 456.20944006301943 chr3 198022430 9494912094 47.94866972392976 37.252343756642254 chr4 191154276 8926413107 46.697428348398546 259.09111527264184 chr5 180915260 8615555386 47.62204905213634 34.465704506224654 chr6 171115067 8195205933 47.89295341829834 103.8649318251207 chr7 159138663 7798635162 49.00528265717552 264.28159408189396 chr8 146364022 7168466774 48.97697313893164 552.3543575553344 chr9 141213431 6165695369 43.662244627425 270.8441520567502 chr10 135534747 7418457483 54.73472778902963 797.6166098039224 chr11 135006516 6702822067 49.648137479527286 146.1660159641735 chr12 133851895 6605987039 49.35295864881106 48.31922523496552 chr13 115169878 4387501245 38.09590946167365 28.396625240156865 chr14 107349540 4495767205 41.879706284721856 45.26280666003269 chr15 102531392 4387885321 42.795530572724495 32.524409374319006 chr16 90354753 4909290510 54.33350595291871 325.0390078705979 chr17 81195210 4626275001 56.97719115450283 153.90842101559613 chr18 78077248 3755644502 48.10165058584032 453.7209143900874 chr19 59128983 3387600506 57.2917093128424 365.4662726892769 chr20 63025520 3207308514 50.88904485040346 53.46487504385994 chr21 48129895 1939732382 40.30202812617813 94.47305616037008 chr22 51304566 2052483113 40.005856652212984 42.1713755819862 chrMT 16571 482242987 29101.62253334138 5546.173239868067 chrX 155270560 6629954841 42.6993683863831 77.22136102156229 chrY 59373566 430474546 7.25027272237615 253.95224380726776