BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695981.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 10,536,127 number of mapped reads = 9,462,216 (89.81%) number of supplementary alignments = 143,748 (1.36%) number of secondary alignments = 0 number of mapped bases = 1,254,837,577 bp number of sequenced bases = 1,245,542,354 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,718,469 duplication rate = 15.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2422 >>>>>>> ACTG content number of A's = 351,418,458 bp (28.21%) number of C's = 270,016,131 bp (21.68%) number of T's = 348,972,108 bp (28.02%) number of G's = 275,135,657 bp (22.09%) number of N's = 0 bp (0%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0178 number of mismatches = 14,105,239 number of insertions = 7,407,419 mapped reads with insertion percentage = 47.45% number of deletions = 8,371,418 mapped reads with deletion percentage = 51.44% homopolymer indels = 36.7% >>>>>>> Coverage mean coverageData = 0.4053X std coverageData = 1.1066X There is a 20.88% of reference with a coverageData >= 1X There is a 9.5% of reference with a coverageData >= 2X There is a 4.54% of reference with a coverageData >= 3X There is a 2.28% of reference with a coverageData >= 4X There is a 1.21% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 146893477 0.5893404654747079 1.673151108039799 chr2 243199373 85678382 0.35229688688383254 0.9600784791468305 chr3 198022430 82188818 0.4150480225901682 1.0329943439021338 chr4 191154276 45401470 0.2375121862301422 0.7679454984769255 chr5 180915260 99764093 0.5514410061373485 1.2774543170246837 chr6 171115067 57143011 0.33394494127159474 0.9347558676589407 chr7 159138663 77775560 0.4887282482698752 1.1331352633459153 chr8 146364022 54306802 0.3710392845039473 0.9820782370653812 chr9 141213431 54304675 0.3845574363248776 1.0205210420022386 chr10 135534747 56801088 0.4190887522002015 1.121850468246621 chr11 135006516 64747125 0.4795851853550535 1.1355151430344692 chr12 133851895 59742265 0.44633111096409955 1.0894272982295832 chr13 115169878 33626438 0.291972506908447 0.8690071509843385 chr14 107349540 26835005 0.2499778294345742 0.7818573581117296 chr15 102531392 47190603 0.4602551675100636 1.1078471064014792 chr16 90354753 52637427 0.5825640074518271 1.2559518529114866 chr17 81195210 42254541 0.5204068195648487 1.2068751802594297 chr18 78077248 21409665 0.2742113169767459 0.9112217838996273 chr19 59128983 29667263 0.5017380901004166 1.4645338884127264 chr20 63025520 44475716 0.7056778904799199 1.4545989104738737 chr21 48129895 9382153 0.19493400099875555 0.7141656057459524 chr22 51304566 15093464 0.2941933862182949 0.8805598382773062 chrMT 16571 208996 12.612153762597309 7.6563643966012584 chrX 155270560 46217621 0.29765862247163916 0.8619286283395184 chrY 59373566 1091919 0.018390658900292428 0.3273824739828603