BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046407.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 10,433,928 number of mapped reads = 10,326,509 (98.97%) number of supplementary alignments = 18,308 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,194,394 number of mapped paired reads (second in pair) = 5,132,115 number of mapped paired reads (both in pair) = 10,249,610 number of mapped paired reads (singletons) = 76,899 number of mapped bases = 975,826,350 bp number of sequenced bases = 975,582,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,940,135 duplication rate = 45.69% >>>>>>> Insert size mean insert size = 18,255.4958 std insert size = 1,362,900.399 median insert size = 120 >>>>>>> Mapping quality mean mapping quality = 53.3829 >>>>>>> ACTG content number of A's = 280,248,460 bp (28.73%) number of C's = 207,965,776 bp (21.32%) number of T's = 276,960,014 bp (28.39%) number of G's = 210,316,116 bp (21.56%) number of N's = 91,776 bp (0.01%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,310,661 number of insertions = 64,074 mapped reads with insertion percentage = 0.61% number of deletions = 90,769 mapped reads with deletion percentage = 0.85% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.3152X std coverageData = 13.0434X There is a 3.53% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129716001 0.5204239832164751 17.555263913626508 chr2 243199373 91457320 0.3760590287377098 14.626245667274812 chr3 198022430 57213802 0.2889258656203744 12.174833357177638 chr4 191154276 29476527 0.15420281260148216 6.708758968775274 chr5 180915260 55885637 0.3089050475896837 12.168921133590244 chr6 171115067 63158879 0.3691017986160155 12.211047782730713 chr7 159138663 65687981 0.41277197986764536 13.993121748885498 chr8 146364022 83821091 0.5726891749394534 21.25956565812536 chr9 141213431 25572649 0.1810921866206905 8.151669888747438 chr10 135534747 30045503 0.22168118261216072 9.224776918746423 chr11 135006516 28870165 0.21384275259721539 8.429304040111855 chr12 133851895 31213214 0.23319217109328186 9.065466112174132 chr13 115169878 25958729 0.2253951245828358 9.655331126181979 chr14 107349540 46075654 0.4292114712368586 18.15458216007757 chr15 102531392 20976093 0.20458215372712388 9.535306401058827 chr16 90354753 48190340 0.5333459325598511 21.627493149950023 chr17 81195210 58841588 0.7246928482603838 21.24987314127478 chr18 78077248 10680108 0.13678899133330108 5.7695030474356885 chr19 59128983 16283635 0.2753917651517869 7.807027468444503 chr20 63025520 20610121 0.32701231183812524 14.953200842378019 chr21 48129895 5530061 0.1148986716052466 8.49338674464798 chr22 51304566 12607844 0.24574506682309719 9.978984841703582 chrMT 16571 658035 39.710035604369075 11.278211229444539 chrX 155270560 16826845 0.10837112328312593 5.892501416390564 chrY 59373566 468528 0.007891188479398391 0.38049980088098934