BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524955.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 = 912,946 number of mapped reads = 850,499 (93.16%) number of supplementary alignments = 2,346 (0.26%) number of secondary alignments = 0 number of mapped bases = 50,302,686 bp number of sequenced bases = 50,285,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,465 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5599 >>>>>>> ACTG content number of A's = 12,335,118 bp (24.53%) number of C's = 9,434,270 bp (18.76%) number of T's = 15,877,433 bp (31.57%) number of G's = 12,638,046 bp (25.13%) number of N's = 634 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 246,985 number of insertions = 3,365 mapped reads with insertion percentage = 0.39% number of deletions = 9,993 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.52% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.1744X There is a 1.52% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5621261 0.02255264591697848 0.30457698595195126 chr2 243199373 3697552 0.015203789197269025 0.1845227699209498 chr3 198022430 2883170 0.014559815269411651 0.1260452559827904 chr4 191154276 3445999 0.018027318415832876 0.1451095713944028 chr5 180915260 2326909 0.01286187245896228 0.11951717279786779 chr6 171115067 3139141 0.01834520510107973 0.1790387613131153 chr7 159138663 3321872 0.020874072569027426 0.2362060314514472 chr8 146364022 3153531 0.021545807206637162 0.18435988463508793 chr9 141213431 1469313 0.010404909714289146 0.1343244944521687 chr10 135534747 2670771 0.01970543391356314 0.1828682949060889 chr11 135006516 2213225 0.016393468001203733 0.1552729029316694 chr12 133851895 2871384 0.021451948812528952 0.15387755554322116 chr13 115169878 1025745 0.00890636525637372 0.10107257539145034 chr14 107349540 1200521 0.011183289653593298 0.1121970069201951 chr15 102531392 1455502 0.014195671897246845 0.13189222280461876 chr16 90354753 1354855 0.014994839286429126 0.1333339604822889 chr17 81195210 1342645 0.01653601240762848 0.16808513743411727 chr18 78077248 1053872 0.013497811808121107 0.20830312770315262 chr19 59128983 1268246 0.021448804556641877 0.21294033798631137 chr20 63025520 964238 0.01529916770222602 0.13075844693727262 chr21 48129895 764835 0.01589105897696224 0.13563359286286028 chr22 51304566 687606 0.013402432836094939 0.11979919411385585 chrMT 16571 3862 0.2330577514935731 0.5114069618874361 chrX 155270560 2230356 0.014364319932896488 0.13566147301542247 chrY 59373566 136275 0.002295213327762729 0.06599239873320092