BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926942.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,891,978 number of mapped reads = 11,688,158 (98.29%) number of supplementary alignments = 75,390 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,872,176 number of mapped paired reads (second in pair) = 5,815,982 number of mapped paired reads (both in pair) = 11,570,500 number of mapped paired reads (singletons) = 117,658 number of mapped bases = 1,099,306,713 bp number of sequenced bases = 1,098,500,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 536,548 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 67,760.4275 std insert size = 2,588,033.2285 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.7105 >>>>>>> ACTG content number of A's = 312,063,873 bp (28.41%) number of C's = 221,061,997 bp (20.12%) number of T's = 315,704,872 bp (28.74%) number of G's = 249,610,500 bp (22.72%) number of N's = 59,290 bp (0.01%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 9,701,856 number of insertions = 170,880 mapped reads with insertion percentage = 1.44% number of deletions = 570,783 mapped reads with deletion percentage = 4.76% homopolymer indels = 53.49% >>>>>>> Coverage mean coverageData = 0.3551X std coverageData = 1.4057X There is a 19.79% of reference with a coverageData >= 1X There is a 8.29% of reference with a coverageData >= 2X There is a 3.54% of reference with a coverageData >= 3X There is a 1.68% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 89692797 0.35984984366398026 1.6438277203078369 chr2 243199373 95257849 0.3916862441910983 2.7650049214288828 chr3 198022430 74821023 0.3778411516311561 0.9324437790051838 chr4 191154276 63384284 0.3315870579845151 0.9322740531575883 chr5 180915260 66995345 0.3703133997651718 0.9159856114464142 chr6 171115067 64766936 0.37849931707065865 1.063581437242911 chr7 159138663 57148917 0.3591139696831561 1.0487357012683378 chr8 146364022 55017074 0.3758920617800459 1.0289214430347633 chr9 141213431 46831626 0.3316371939153578 1.5787123685401407 chr10 135534747 54450715 0.40174727297052465 2.0695528720120775 chr11 135006516 52380060 0.38798171786019575 1.2875919917843395 chr12 133851895 49525961 0.3700056767967312 0.9376818171566584 chr13 115169878 32844506 0.28518312748408053 0.8040150838041659 chr14 107349540 34070794 0.3173818350781941 0.8874881977591522 chr15 102531392 33369874 0.3254600698291505 0.8851824706053655 chr16 90354753 35139622 0.3889072885850288 1.8633371175512974 chr17 81195210 29347334 0.36144169095689266 1.047969943955564 chr18 78077248 29550731 0.37848069388921085 1.6693887728333578 chr19 59128983 17402986 0.29432243067667846 1.1572718888422544 chr20 63025520 27235363 0.43213230132809693 1.0633402264324276 chr21 48129895 14374887 0.2986685717889058 1.1186686122047844 chr22 51304566 15134727 0.294997661611639 0.8798022095580287 chrMT 16571 95610 5.769718182366785 5.134140979227188 chrX 155270560 58960520 0.37972761868057925 1.0066427437642091 chrY 59373566 1507172 0.025384562550950705 0.5587893066667877