BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013241.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 = 2,123,519 number of mapped reads = 1,882,663 (88.66%) number of supplementary alignments = 21,804 (1.03%) number of secondary alignments = 0 number of mapped bases = 123,383,019 bp number of sequenced bases = 123,317,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,034 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8111 >>>>>>> ACTG content number of A's = 33,635,753 bp (27.28%) number of C's = 23,200,927 bp (18.81%) number of T's = 38,629,883 bp (31.33%) number of G's = 27,836,423 bp (22.57%) number of N's = 14,377 bp (0.01%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 989,298 number of insertions = 8,424 mapped reads with insertion percentage = 0.44% number of deletions = 38,411 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.4053X There is a 3.16% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 6990628 0.028046582078525693 0.7867102716465367 chr2 243199373 13579479 0.055836817474031894 0.5070532551026806 chr3 198022430 5320149 0.02686639589262691 0.1941389077261337 chr4 191154276 5118476 0.026776675401182237 0.2082502211085726 chr5 180915260 6386318 0.035300051526886124 0.2308539941377484 chr6 171115067 5000548 0.029223306209499367 0.23896782535079758 chr7 159138663 10579304 0.06647852759703027 0.5432359255382733 chr8 146364022 12923041 0.08829383630903502 0.536078688511698 chr9 141213431 3355467 0.023761670375390852 0.2987966379254384 chr10 135534747 8240144 0.06079728027234226 0.43866725410108076 chr11 135006516 7343338 0.05439247095303163 0.3905478967193627 chr12 133851895 3193837 0.023860977089640755 0.18916311284216472 chr13 115169878 388760 0.003375535398240154 0.06772339624675763 chr14 107349540 2377558 0.022147817307833828 0.1845977335174519 chr15 102531392 887295 0.008653886216623295 0.10940337143394747 chr16 90354753 6840060 0.07570227102496756 0.35217329604607106 chr17 81195210 5509181 0.06785105919425542 0.4066053963444116 chr18 78077248 3416988 0.04376419619707908 0.4814026223913929 chr19 59128983 2995349 0.050657881262730325 0.7253848842798576 chr20 63025520 3430946 0.05443740884644823 0.28871619585629965 chr21 48129895 3753112 0.07797881129805083 0.34848933909358787 chr22 51304566 1550908 0.030229434159914734 0.2067992094629869 chrMT 16571 9298 0.5611007181220204 0.8857852340855474 chrX 155270560 3969810 0.025567048898387436 0.23646844780322207 chrY 59373566 223025 0.0037563012469219044 0.10437667988879104