BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524424.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 = 3,103,927 number of mapped reads = 2,853,046 (91.92%) number of supplementary alignments = 12,129 (0.39%) number of secondary alignments = 0 number of mapped bases = 166,318,944 bp number of sequenced bases = 166,271,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,670 duplication rate = 5.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.578 >>>>>>> ACTG content number of A's = 41,477,109 bp (24.95%) number of C's = 32,014,341 bp (19.25%) number of T's = 52,825,988 bp (31.77%) number of G's = 39,937,441 bp (24.02%) number of N's = 17,007 bp (0.01%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 844,398 number of insertions = 12,522 mapped reads with insertion percentage = 0.44% number of deletions = 28,921 mapped reads with deletion percentage = 1.01% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.5183X There is a 4.43% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13557177 0.05439174813530354 1.07193401657071 chr2 243199373 13944195 0.057336475945602046 0.7328629988970156 chr3 198022430 10779461 0.05443555560852374 0.28069203483327987 chr4 191154276 10510657 0.05498520472542293 0.4071652083052398 chr5 180915260 9735381 0.05381182880869198 0.2753079222945751 chr6 171115067 9297482 0.05433467761199544 0.31977299636534084 chr7 159138663 9141843 0.057445769793855815 0.6643818558890591 chr8 146364022 8303026 0.056728599600795335 0.3700688965564084 chr9 141213431 6989697 0.04949739518757249 0.3624021533526016 chr10 135534747 8117744 0.05989419082325804 0.571050964881914 chr11 135006516 7586668 0.05619482840368979 0.3939019992925438 chr12 133851895 7478301 0.055869967324706164 0.29082675568602995 chr13 115169878 5040872 0.04376901397776943 0.2496925412169843 chr14 107349540 4960075 0.04620490222873801 0.2751811764957168 chr15 102531392 4967714 0.04845066377329589 0.26333349123104355 chr16 90354753 5125845 0.0567302198258458 0.3174055652746644 chr17 81195210 4751828 0.058523501571090215 0.3253325803176627 chr18 78077248 4369801 0.055967661667583365 0.7280325831395689 chr19 59128983 3741141 0.06327084976245913 0.6883707971348028 chr20 63025520 3720132 0.059025804150445726 0.31352773284152474 chr21 48129895 2247897 0.046704797506830216 0.35665024987909405 chr22 51304566 2142021 0.04175107923142747 0.24787249316202342 chrMT 16571 12940 0.7808822641964879 1.0505452613323776 chrX 155270560 9136783 0.05884427157343929 0.33516878373462883 chrY 59373566 660263 0.011120487524700807 0.37235986088396383