BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524933.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 = 1,993,175 number of mapped reads = 1,820,921 (91.36%) number of supplementary alignments = 7,559 (0.38%) number of secondary alignments = 0 number of mapped bases = 104,958,911 bp number of sequenced bases = 104,931,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,870 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2119 >>>>>>> ACTG content number of A's = 27,017,838 bp (25.75%) number of C's = 20,527,441 bp (19.56%) number of T's = 32,715,356 bp (31.18%) number of G's = 24,667,171 bp (23.51%) number of N's = 3,297 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 504,914 number of insertions = 6,347 mapped reads with insertion percentage = 0.35% number of deletions = 16,956 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.61% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.3001X There is a 3.01% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 7557629 0.030321404896319196 0.5146935972373357 chr2 243199373 8863305 0.03644460464953583 0.33542704053931394 chr3 198022430 6296473 0.03179676665921128 0.1941340624010983 chr4 191154276 6481219 0.033905697197168634 0.22663561348219569 chr5 180915260 5789996 0.03200391166560521 0.19572613016080356 chr6 171115067 4888074 0.028566005821100488 0.2058010596572966 chr7 159138663 6784310 0.042631437716678565 0.41682817814393813 chr8 146364022 4520276 0.030883791919847626 0.28531819108666184 chr9 141213431 4858407 0.03440470899683756 0.2925161432100999 chr10 135534747 3999340 0.029507857494285212 0.2799536408456871 chr11 135006516 4033659 0.029877513467572187 0.2525924879369136 chr12 133851895 7820419 0.058425911713838645 0.2986064046023526 chr13 115169878 3926744 0.034095234519567696 0.20086179129194456 chr14 107349540 3707465 0.034536384599319195 0.21847552309826726 chr15 102531392 2724328 0.0265706721313215 0.17787223344497827 chr16 90354753 3027406 0.0335057747321826 0.2162199379089356 chr17 81195210 3199236 0.039401782445048175 0.22721437210704126 chr18 78077248 3287193 0.042101804100472394 0.5421510226491658 chr19 59128983 1824224 0.030851604533769842 0.39524529244756157 chr20 63025520 3288269 0.052173611578294 0.2579121503231184 chr21 48129895 1279008 0.02657408664614789 0.20553071347874508 chr22 51304566 1054735 0.0205583066427265 0.15471543988685774 chrMT 16571 7968 0.48084002172469975 0.7868859841475281 chrX 155270560 5435272 0.03500516775362954 0.23835581339482098 chrY 59373566 303956 0.00511938258854117 0.1313460154957298