BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234089.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 = 2,957,946 number of mapped reads = 2,406,965 (81.37%) number of supplementary alignments = 16,238 (0.55%) number of secondary alignments = 0 number of mapped bases = 151,869,184 bp number of sequenced bases = 151,775,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,686 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2143 >>>>>>> ACTG content number of A's = 40,859,555 bp (26.92%) number of C's = 27,890,736 bp (18.38%) number of T's = 47,666,284 bp (31.41%) number of G's = 35,337,616 bp (23.28%) number of N's = 21,036 bp (0.01%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,287,156 number of insertions = 11,070 mapped reads with insertion percentage = 0.46% number of deletions = 54,088 mapped reads with deletion percentage = 2.21% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.4553X There is a 4.01% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 16512730 0.06624950394807642 0.9213058523883613 chr2 243199373 9700433 0.03988675168171589 0.5705615515087625 chr3 198022430 14061660 0.07101044058493777 0.3179333721579574 chr4 191154276 5218852 0.027301780055393583 0.2264091238631692 chr5 180915260 11256316 0.06221872052141981 0.2979126627726445 chr6 171115067 9858322 0.05761223820226187 0.37545865302361925 chr7 159138663 8979411 0.0564250750303212 0.5521656133131256 chr8 146364022 9296876 0.06351886121303772 0.6130296299838907 chr9 141213431 7734860 0.0547742516078375 0.3728065259330207 chr10 135534747 5721586 0.04221490154107861 0.4194518367465187 chr11 135006516 5310158 0.03933260524995697 0.29523753396382313 chr12 133851895 5456556 0.04076562382624467 0.2425414019578906 chr13 115169878 7010704 0.060872722292889814 0.2931703048834285 chr14 107349540 6015138 0.05603319772026969 0.3030751616113702 chr15 102531392 2822794 0.02753102191375691 0.20467088432181824 chr16 90354753 3801562 0.0420737357336365 0.2784221780789408 chr17 81195210 3815636 0.04699336327844955 0.27383907954932324 chr18 78077248 3648188 0.046725366139954115 0.6469141364095037 chr19 59128983 3915634 0.06622190677624204 0.6261774402428514 chr20 63025520 2990448 0.04744820828134381 0.27448575201987463 chr21 48129895 1975610 0.04104746125043489 0.258996813608766 chr22 51304566 1318408 0.025697673770400865 0.18675355559915705 chrMT 16571 23183 1.399010319232394 1.5786406644790132 chrX 155270560 5025009 0.03236292185717627 0.24533725146269725 chrY 59373566 399110 0.006722014978854394 0.16423012910264828