BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777255.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 20,445,112 number of mapped reads = 20,284,519 (99.21%) number of supplementary alignments = 824,577 (4.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,144,128 number of mapped paired reads (second in pair) = 10,140,391 number of mapped paired reads (both in pair) = 20,213,758 number of mapped paired reads (singletons) = 70,761 number of mapped bases = 2,007,488,919 bp number of sequenced bases = 2,006,433,567 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,962,831 duplication rate = 31.06% >>>>>>> Insert size mean insert size = 246,708.3789 std insert size = 3,575,720.9631 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.5267 >>>>>>> ACTG content number of A's = 548,572,817 bp (27.34%) number of C's = 453,465,278 bp (22.6%) number of T's = 547,064,945 bp (27.27%) number of G's = 457,255,417 bp (22.79%) number of N's = 75,110 bp (0%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 7,127,638 number of insertions = 477,371 mapped reads with insertion percentage = 2.24% number of deletions = 337,743 mapped reads with deletion percentage = 1.5% homopolymer indels = 36.31% >>>>>>> Coverage mean coverageData = 0.6485X std coverageData = 33.1015X There is a 9.88% of reference with a coverageData >= 1X There is a 4.94% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 2.43% of reference with a coverageData >= 4X There is a 2.04% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.63% of reference with a coverageData >= 7X There is a 1.5% of reference with a coverageData >= 8X There is a 1.39% of reference with a coverageData >= 9X There is a 1.29% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1.13% of reference with a coverageData >= 12X There is a 1.07% of reference with a coverageData >= 13X There is a 1.01% of reference with a coverageData >= 14X There is a 0.95% of reference with a coverageData >= 15X There is a 0.9% of reference with a coverageData >= 16X There is a 0.85% of reference with a coverageData >= 17X There is a 0.81% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.67% of reference with a coverageData >= 22X There is a 0.64% of reference with a coverageData >= 23X There is a 0.61% of reference with a coverageData >= 24X There is a 0.59% of reference with a coverageData >= 25X There is a 0.56% of reference with a coverageData >= 26X There is a 0.54% of reference with a coverageData >= 27X There is a 0.52% of reference with a coverageData >= 28X There is a 0.5% of reference with a coverageData >= 29X There is a 0.48% of reference with a coverageData >= 30X There is a 0.46% of reference with a coverageData >= 31X There is a 0.44% of reference with a coverageData >= 32X There is a 0.43% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.38% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.36% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.3% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189997374 0.7622744257876894 6.360142746573109 chr2 243199373 170858953 0.7025468482601721 6.200737302271191 chr3 198022430 115875018 0.585161074934794 5.537773782837903 chr4 191154276 90910952 0.47558942390595543 22.377010272905064 chr5 180915260 95205253 0.526242247337234 4.96860608227503 chr6 171115067 87247849 0.5098782388344564 4.978551711142175 chr7 159138663 124404435 0.7817360825759859 9.487632342791285 chr8 146364022 65323709 0.4463098793499949 5.059851101634092 chr9 141213431 134611515 0.9532486679684172 150.2416805349759 chr10 135534747 84787910 0.6255806121805798 5.764462162929826 chr11 135006516 133586145 0.9894792411352945 8.176806174537289 chr12 133851895 108801930 0.8128531164986494 6.6214956006412695 chr13 115169878 54004384 0.46891066429713507 5.112085236609382 chr14 107349540 41335299 0.38505334070364905 3.951857032040923 chr15 102531392 97924124 0.9550648059084188 8.316504998383873 chr16 90354753 59172378 0.6548894887687867 5.362344539866595 chr17 81195210 81404678 1.002579807355631 7.751366575686634 chr18 78077248 29410130 0.37667990039812876 5.336225918488906 chr19 59128983 97040985 1.6411745996037173 11.630420711313304 chr20 63025520 52634170 0.8351247240800235 6.781129891295636 chr21 48129895 12897725 0.26797741819299625 3.430231132330486 chr22 51304566 21355166 0.4162429909259928 3.9509677516689568 chrMT 16571 753458 45.468469012129624 21.17703319708286 chrX 155270560 57007440 0.3671490590360465 4.4020635410563145 chrY 59373566 937939 0.015797248896924937 0.7506267923069513