BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975237.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 4,128,310 number of mapped reads = 4,085,385 (98.96%) number of supplementary alignments = 33,549 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,042,201 number of mapped paired reads (second in pair) = 2,043,184 number of mapped paired reads (both in pair) = 4,071,566 number of mapped paired reads (singletons) = 13,819 number of mapped bases = 384,406,399 bp number of sequenced bases = 384,150,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,038 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 111,099.9355 std insert size = 3,214,888.9794 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.786 >>>>>>> ACTG content number of A's = 112,536,093 bp (29.29%) number of C's = 78,116,000 bp (20.33%) number of T's = 113,565,112 bp (29.56%) number of G's = 79,927,702 bp (20.81%) number of N's = 5,365 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,252,156 number of insertions = 76,559 mapped reads with insertion percentage = 1.82% number of deletions = 147,000 mapped reads with deletion percentage = 3.52% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.1242X std coverageData = 1.1821X There is a 8.55% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 26326324 0.10562189933320167 1.57790381535417 chr2 243199373 40153819 0.16510658931674138 1.7867680844316896 chr3 198022430 23689280 0.11962927634005906 0.45420052893661256 chr4 191154276 19265305 0.10078406511816665 0.9069736471863246 chr5 180915260 23152875 0.12797635202248833 0.4806055796413134 chr6 171115067 18354568 0.10726447601484444 0.5844562451805442 chr7 159138663 15316632 0.0962470823322174 0.882055429285051 chr8 146364022 21384746 0.14610657528938362 0.6132431938682797 chr9 141213431 17214822 0.12190640704707473 1.696209491718245 chr10 135534747 19001769 0.14019850570127232 2.327016989922434 chr11 135006516 22643135 0.16771883069703095 0.9283274430825587 chr12 133851895 20900170 0.15614399781190993 0.5137501811244085 chr13 115169878 9408188 0.08168965847128883 0.35793229125141335 chr14 107349540 13393767 0.12476780990398283 0.49717280424195404 chr15 102531392 8428902 0.08220801293715002 0.36252459587894204 chr16 90354753 10683159 0.11823571694119954 1.651149096109554 chr17 81195210 11040789 0.13597832926351197 2.1289775057473803 chr18 78077248 12672900 0.16231232945095606 1.5515695663055118 chr19 59128983 7143368 0.12080992497368 0.7656004488355096 chr20 63025520 19983569 0.31707106898919674 0.8078177690549957 chr21 48129895 3759296 0.07810729693052519 0.46615033192080063 chr22 51304566 3514984 0.06851210864935492 0.3702824051667619 chrMT 16571 95205 5.745277895117977 4.1229470171801 chrX 155270560 11061594 0.07124076837231733 0.4529832871201056 chrY 59373566 5817233 0.09797681682114226 1.7026380619473853