BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,947,380 number of mapped reads = 1,704,203 (87.51%) number of supplementary alignments = 6,129 (0.31%) number of secondary alignments = 0 number of mapped bases = 96,199,416 bp number of sequenced bases = 96,170,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,179 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9325 >>>>>>> ACTG content number of A's = 23,719,582 bp (24.66%) number of C's = 18,164,826 bp (18.89%) number of T's = 30,769,790 bp (31.99%) number of G's = 23,515,850 bp (24.45%) number of N's = 680 bp (0%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 514,373 number of insertions = 6,993 mapped reads with insertion percentage = 0.41% number of deletions = 18,012 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2566X There is a 2.79% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8110835 0.03254088181389125 0.3176405488491836 chr2 243199373 7611909 0.03129904862049131 0.3699300547972227 chr3 198022430 5590675 0.0282325340619242 0.1865183143909072 chr4 191154276 5962840 0.031193861444145776 0.21234014421339753 chr5 180915260 5507697 0.03044351814214014 0.18916773234538312 chr6 171115067 5166240 0.030191613693491996 0.22450150207627184 chr7 159138663 5480301 0.03443726933912974 0.3780753649950187 chr8 146364022 5003214 0.03418335962371955 0.24909355164585759 chr9 141213431 3217560 0.022785084798343295 0.19504798355083874 chr10 135534747 4303770 0.03175399737161128 0.3313360895708432 chr11 135006516 3438459 0.025468837370782902 0.215935854768574 chr12 133851895 4808037 0.03592057475166863 0.20865985611535365 chr13 115169878 2947165 0.02558972060385442 0.1771536968607011 chr14 107349540 3210142 0.029903640015597643 0.19476687131811882 chr15 102531392 3533782 0.03446536647039767 0.20826913927238278 chr16 90354753 3360936 0.03719711347116405 0.22504486520930142 chr17 81195210 4302172 0.052985539417904085 0.26568781504922384 chr18 78077248 1784655 0.022857555122844493 0.2997171419284274 chr19 59128983 2469542 0.0417653386664878 0.32750266362593944 chr20 63025520 2769517 0.043942786985335464 0.2399826893906197 chr21 48129895 1183898 0.024597975956523487 0.18369312444781893 chr22 51304566 893186 0.017409483592551976 0.14412897565014168 chrMT 16571 6833 0.41234687103976825 0.6884231018484245 chrX 155270560 5241638 0.033758092970103286 0.21493181007508053 chrY 59373566 294413 0.004958654496177642 0.1379548610428897