BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716450.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 = 1,687,282 number of mapped reads = 1,456,984 (86.35%) number of supplementary alignments = 21,768 (1.29%) number of secondary alignments = 0 number of mapped bases = 113,511,678 bp number of sequenced bases = 113,462,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,707 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.784 >>>>>>> ACTG content number of A's = 27,979,517 bp (24.66%) number of C's = 20,723,056 bp (18.26%) number of T's = 36,511,775 bp (32.18%) number of G's = 28,242,053 bp (24.89%) number of N's = 6,448 bp (0.01%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 979,821 number of insertions = 10,175 mapped reads with insertion percentage = 0.69% number of deletions = 28,038 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.4034X There is a 3.17% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 9242418 0.0370808223583122 0.5965260188333613 chr2 243199373 9852897 0.04051366119270382 0.6327213667517533 chr3 198022430 7775879 0.03926766780914667 0.22267764911588944 chr4 191154276 7332621 0.038359701668405265 0.2427515630624384 chr5 180915260 7007399 0.038733045515342374 0.22663523457788315 chr6 171115067 6745297 0.03941965554675556 0.2835605749562911 chr7 159138663 6523125 0.040990196078246555 0.5367639659801513 chr8 146364022 5985246 0.04089287734932564 0.5286312438875762 chr9 141213431 4981948 0.035279562041092255 0.4572714874985337 chr10 135534747 5609139 0.04138524713518667 0.379344605809085 chr11 135006516 5294006 0.039212966580072325 0.4060233730643359 chr12 133851895 5330230 0.03982184936567391 0.22982109604229387 chr13 115169878 3564105 0.03094650321675256 0.19497657932863802 chr14 107349540 3530585 0.03288868308145522 0.28031857830565676 chr15 102531392 3338548 0.03256122768722383 0.20755111324201717 chr16 90354753 3466994 0.03837090894377189 0.25357043450141475 chr17 81195210 3144707 0.03873020341963522 0.24042515474973017 chr18 78077248 3158629 0.040455178440715535 0.8020957636740503 chr19 59128983 2438347 0.041237763213346657 0.45426803158521895 chr20 63025520 2396048 0.03801710799054098 0.23233236773248706 chr21 48129895 1515084 0.031479063064650356 0.21901570450813065 chr22 51304566 1320341 0.02573535072882207 0.18015787742358574 chrMT 16571 16192 0.977128718846177 1.3843049731454367 chrX 155270560 3660338 0.023573934427749858 0.2458674158123611 chrY 59373566 281555 0.004742093476413392 0.14955897315364314