BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472662.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,631,238 number of mapped reads = 17,473,388 (99.1%) number of supplementary alignments = 107,379 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,758,942 number of mapped paired reads (second in pair) = 8,714,446 number of mapped paired reads (both in pair) = 17,369,134 number of mapped paired reads (singletons) = 104,254 number of mapped bases = 1,717,749,589 bp number of sequenced bases = 1,717,517,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,335,089 duplication rate = 49.74% >>>>>>> Insert size mean insert size = 27,518.406 std insert size = 1,701,420.3929 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 54.5637 >>>>>>> ACTG content number of A's = 466,076,600 bp (27.14%) number of C's = 394,928,644 bp (22.99%) number of T's = 466,847,437 bp (27.18%) number of G's = 389,342,124 bp (22.67%) number of N's = 322,403 bp (0.02%) GC percentage = 45.66% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,830,319 number of insertions = 114,784 mapped reads with insertion percentage = 0.65% number of deletions = 98,055 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.5549X std coverageData = 28.4249X There is a 3.33% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167912816 0.673670602409452 23.939508763074397 chr2 243199373 138857249 0.5709605550668916 29.79046411678834 chr3 198022430 153924067 0.7773062223304703 23.719687441809224 chr4 191154276 31713832 0.16590699754997895 8.035228286068865 chr5 180915260 84738837 0.46838965933553645 28.088782302866726 chr6 171115067 151024981 0.8825931208033247 30.514720976345068 chr7 159138663 110655698 0.6953413828794075 31.612855218836685 chr8 146364022 78026094 0.5330961320535452 21.756403312095788 chr9 141213431 124777847 0.8836117507831107 32.417911270377175 chr10 135534747 25576656 0.1887092171279148 7.704475750732367 chr11 135006516 60186126 0.4458016381964853 43.37090560040537 chr12 133851895 54066596 0.4039285062045629 14.270285071524142 chr13 115169878 54907546 0.4767526627057814 27.809672151754622 chr14 107349540 20403393 0.190065024964243 7.021638358699037 chr15 102531392 19252581 0.18777255067404136 11.42712802398276 chr16 90354753 138953423 1.5378651192815502 89.03112097377439 chr17 81195210 49265607 0.6067550906020195 17.718177428514682 chr18 78077248 4871746 0.0623964871302841 2.4750749466850475 chr19 59128983 54684251 0.9248298926433421 27.614221724468685 chr20 63025520 65619851 1.0411631827869092 30.285650567332727 chr21 48129895 14201770 0.2950717012783843 23.06412410074908 chr22 51304566 25574552 0.4984849106802697 18.914259641644158 chrMT 16571 9084 0.5481865910325266 1.1822712615310795 chrX 155270560 87433018 0.5631010669376088 18.577922289587157 chrY 59373566 1111968 0.018728334424110555 1.384557887309658