BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230391.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 = 1,643,279 number of mapped reads = 1,020,309 (62.09%) number of supplementary alignments = 5,225 (0.32%) number of secondary alignments = 0 number of mapped bases = 63,350,196 bp number of sequenced bases = 63,317,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,809 duplication rate = 6.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9717 >>>>>>> ACTG content number of A's = 16,337,260 bp (25.8%) number of C's = 10,482,811 bp (16.56%) number of T's = 21,747,326 bp (34.35%) number of G's = 14,644,715 bp (23.13%) number of N's = 105,601 bp (0.17%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 680,503 number of insertions = 5,371 mapped reads with insertion percentage = 0.52% number of deletions = 20,331 mapped reads with deletion percentage = 1.97% homopolymer indels = 49.67% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2243X There is a 1.58% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.09% 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% 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 6379104 0.025593131822126934 0.38053053406162385 chr2 243199373 4803559 0.019751527073221524 0.2273813137464377 chr3 198022430 4112456 0.020767627182435848 0.1820194148543262 chr4 191154276 4284900 0.022415925448615127 0.192333174648012 chr5 180915260 4391512 0.024273861696354416 0.19734966910180526 chr6 171115067 3452100 0.02017414398698158 0.20412683195567657 chr7 159138663 3204179 0.020134509990196413 0.237356128039705 chr8 146364022 3958145 0.027043155455238856 0.2880135013763443 chr9 141213431 2636805 0.018672480240211713 0.20433112540413456 chr10 135534747 2647077 0.019530615274620317 0.20763497122487226 chr11 135006516 2835939 0.02100594166877101 0.2056980785471246 chr12 133851895 3034161 0.022668046649619716 0.19147734677463313 chr13 115169878 2133067 0.018521049401476312 0.17319316297554627 chr14 107349540 1619074 0.01508226304462972 0.15948493627971627 chr15 102531392 1688322 0.016466391093178566 0.16256002474484402 chr16 90354753 1509262 0.01670373665898904 0.16503757804160277 chr17 81195210 1514379 0.0186510879151615 0.17777883034436381 chr18 78077248 1148631 0.014711468826360274 0.2802404291762449 chr19 59128983 1028196 0.017389035762715555 0.2491388373477683 chr20 63025520 1203505 0.019095518767635714 0.17473994194805129 chr21 48129895 858932 0.017846122456739204 0.17179380290160634 chr22 51304566 686477 0.01338042699747231 0.1441008711627383 chrMT 16571 49854 3.0085088407458813 2.9113796075079805 chrX 155270560 4000727 0.025766165846249283 0.21221490821275393 chrY 59373566 169833 0.0028604143466808107 0.07596589126576032