BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525129.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 = 1,412,516 number of mapped reads = 1,267,189 (89.71%) number of supplementary alignments = 30,727 (2.18%) number of secondary alignments = 0 number of mapped bases = 96,258,327 bp number of sequenced bases = 96,219,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,744 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.978 >>>>>>> ACTG content number of A's = 25,166,162 bp (26.15%) number of C's = 18,373,653 bp (19.1%) number of T's = 30,083,191 bp (31.27%) number of G's = 22,593,353 bp (23.48%) number of N's = 3,550 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 726,902 number of insertions = 8,243 mapped reads with insertion percentage = 0.64% number of deletions = 22,604 mapped reads with deletion percentage = 1.76% homopolymer indels = 42.19% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.3477X There is a 2.77% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 9270463 0.037193339630636264 0.626800159486439 chr2 243199373 7993396 0.03286766697379602 0.48101185820118153 chr3 198022430 6161085 0.031113066332940163 0.19139782523897814 chr4 191154276 6105076 0.031937951521419275 0.20264163383421316 chr5 180915260 5694327 0.03147510608005096 0.19524097054286332 chr6 171115067 5381778 0.03145122223515244 0.22155421662858193 chr7 159138663 5212665 0.03275549072572012 0.473505746900377 chr8 146364022 4833264 0.03302221361476388 0.44926464938857014 chr9 141213431 3897675 0.027601305147808498 0.29987488194726775 chr10 135534747 4391522 0.032401447578605067 0.347291646595429 chr11 135006516 5236475 0.038786831592632166 0.37414779079535365 chr12 133851895 4183098 0.031251690534526984 0.19276527030003582 chr13 115169878 3544820 0.030779054919203786 0.19079863321194332 chr14 107349540 2831957 0.02638070922334646 0.2072710740669352 chr15 102531392 2648079 0.025827007205754118 0.17351932292773717 chr16 90354753 2086234 0.023089366422151585 0.18274947823561283 chr17 81195210 2754615 0.033925831339065446 0.23388495088491074 chr18 78077248 2554697 0.03272012097557537 0.5452152740331688 chr19 59128983 1800577 0.03045168221479473 0.4421347482500342 chr20 63025520 1855556 0.02944134376043228 0.19140738074680247 chr21 48129895 1239892 0.02576136931111111 0.18877105198241084 chr22 51304566 957425 0.018661594369592756 0.1481347013925064 chrMT 16571 20397 1.2308852815159013 1.663021040132282 chrX 155270560 5378769 0.03464126747530247 0.2721153605475884 chrY 59373566 224485 0.0037808913144950734 0.09315171051428098