BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525065.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 = 1,158,297 number of mapped reads = 1,044,355 (90.16%) number of supplementary alignments = 3,178 (0.27%) number of secondary alignments = 0 number of mapped bases = 60,777,900 bp number of sequenced bases = 60,758,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,358 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2042 >>>>>>> ACTG content number of A's = 15,212,737 bp (25.04%) number of C's = 10,634,370 bp (17.5%) number of T's = 19,286,076 bp (31.74%) number of G's = 15,618,819 bp (25.71%) number of N's = 6,877 bp (0.01%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 294,879 number of insertions = 3,747 mapped reads with insertion percentage = 0.36% number of deletions = 11,930 mapped reads with deletion percentage = 1.13% homopolymer indels = 45.12% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2071X There is a 1.76% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4849649 0.019456918424287498 0.3676880342346459 chr2 243199373 5044858 0.020743713019358814 0.2401244911439934 chr3 198022430 4095957 0.02068430833820189 0.15807759220152223 chr4 191154276 3976805 0.020804164485444206 0.17226788182132893 chr5 180915260 3720888 0.020567021267304926 0.15669750828236265 chr6 171115067 3453853 0.02018438855533394 0.16290715260894742 chr7 159138663 3327251 0.0209078732802977 0.2346696979563107 chr8 146364022 2986797 0.020406633810595886 0.2159770763666606 chr9 141213431 2540384 0.017989676916779964 0.17085273814962057 chr10 135534747 3153260 0.02326532545930823 0.23512376938319798 chr11 135006516 2730432 0.020224446055625938 0.17816408221684768 chr12 133851895 2683782 0.0200503847928339 0.15781984818056116 chr13 115169878 1885015 0.016367257070464207 0.13905968416077275 chr14 107349540 1900003 0.017699218832237195 0.14789232423873885 chr15 102531392 1729039 0.016863508495037306 0.14117804949972018 chr16 90354753 1763045 0.01951247656003221 0.16250188276441063 chr17 81195210 1606444 0.01978496022117561 0.15892991744821405 chr18 78077248 1597657 0.020462516814117218 0.26779352675257534 chr19 59128983 1199084 0.02027912436782483 0.2702846028033282 chr20 63025520 1322878 0.020989561053998445 0.1610376787704972 chr21 48129895 858597 0.01783916212574326 0.1628598727653857 chr22 51304566 715857 0.01395308557916658 0.12944306182692988 chrMT 16571 15692 0.946955524711846 1.1959960714555575 chrX 155270560 3407329 0.021944462620602387 0.17556698374061058 chrY 59373566 213344 0.0035932488878973514 0.13026203674690304