BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231751.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,923,684 number of mapped reads = 4,540,087 (92.21%) number of supplementary alignments = 28,567 (0.58%) number of secondary alignments = 0 number of mapped bases = 310,796,406 bp number of sequenced bases = 310,688,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 635,344 duplication rate = 6.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.6895 >>>>>>> ACTG content number of A's = 81,641,375 bp (26.28%) number of C's = 56,725,856 bp (18.26%) number of T's = 88,855,072 bp (28.6%) number of G's = 83,401,031 bp (26.84%) number of N's = 65,545 bp (0.02%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,040,663 number of insertions = 21,918 mapped reads with insertion percentage = 0.48% number of deletions = 63,806 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.1004X std coverageData = 37.6254X There is a 5.08% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 64495354 0.2587570443806437 1.6676807823194189 chr2 243199373 23713648 0.09750702770109526 134.205466937545 chr3 198022430 22656640 0.11441451354778345 0.5605984404244906 chr4 191154276 3338682 0.017465902776875365 0.3232966903850731 chr5 180915260 21744521 0.12019174612467738 0.5689616020673101 chr6 171115067 33228373 0.19418730087631617 1.0723091479442854 chr7 159138663 2285979 0.014364699042369106 0.46402067277964093 chr8 146364022 3115518 0.021286091741862627 0.9290716000919462 chr9 141213431 14056796 0.09954291104222232 0.9536737728213126 chr10 135534747 24454232 0.18042776882890407 1.0816296517577835 chr11 135006516 10323846 0.07646924241789929 0.7900957041600836 chr12 133851895 23721289 0.17722041962872473 0.714452684944359 chr13 115169878 878357 0.00762662091211037 0.13515132446314845 chr14 107349540 16256293 0.15143328047796012 0.7608433174034189 chr15 102531392 1474943 0.01438528211925573 0.2396897186432355 chr16 90354753 4311233 0.04771451259459478 0.5133821311591056 chr17 81195210 1839600 0.022656508924602817 0.3581408571239514 chr18 78077248 24567922 0.3146617309052696 1.7050730808322259 chr19 59128983 2313075 0.03911914060825298 1.4326754596364204 chr20 63025520 4224100 0.06702205709687123 0.44984778436451495 chr21 48129895 2990682 0.06213772126450723 0.4804357362619577 chr22 51304566 1972255 0.03844209499793839 0.3145718810100737 chrMT 16571 12247 0.739062217126305 1.2378717798853927 chrX 155270560 2150015 0.013846894092479604 0.6207199854767674 chrY 59373566 670806 0.011298058129100752 0.3596083079313557