BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093992.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 356,172 number of mapped reads = 338,892 (95.15%) number of supplementary alignments = 24,539 (6.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 170,397 number of mapped paired reads (second in pair) = 168,495 number of mapped paired reads (both in pair) = 335,652 number of mapped paired reads (singletons) = 3,240 number of mapped bases = 42,885,860 bp number of sequenced bases = 42,126,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 319,015 duplication rate = 51.76% >>>>>>> Insert size mean insert size = 1,362,494.9498 std insert size = 10,568,017.6435 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 41.81 >>>>>>> ACTG content number of A's = 11,078,718 bp (26.3%) number of C's = 9,895,261 bp (23.49%) number of T's = 10,452,966 bp (24.81%) number of G's = 10,699,199 bp (25.4%) number of N's = 450 bp (0%) GC percentage = 48.89% >>>>>>> Mismatches and indels general error rate = 0.0348 number of mismatches = 1,419,336 number of insertions = 22,820 mapped reads with insertion percentage = 6.6% number of deletions = 113,690 mapped reads with deletion percentage = 32.23% homopolymer indels = 30.19% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 2.4754X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 714463 0.0028664442123897457 0.9075462022979343 chr2 243199373 2064858 0.008490391955081233 2.6101048355492322 chr3 198022430 795898 0.004019231558768368 1.3488285849471209 chr4 191154276 985155 0.005153716781098844 1.5769380704790272 chr5 180915260 384120 0.002123203979586907 0.9578789789491322 chr6 171115067 834703 0.004878021641425649 1.3228504154309124 chr7 159138663 887990 0.005579976501373522 1.5580224633316462 chr8 146364022 421719 0.0028813023462828866 0.7842212476537253 chr9 141213431 646684 0.004579479412266387 1.4235075823959016 chr10 135534747 739023 0.005452646028844544 1.5078489523841792 chr11 135006516 1016381 0.007528384778109525 1.7885597334824388 chr12 133851895 966963 0.007224126337546435 1.6541689487773998 chr13 115169878 883665 0.007672709352006086 1.9942599772345753 chr14 107349540 195931 0.0018251685102702816 0.5632946001954793 chr15 102531392 607704 0.005927004287623443 1.4884196581462612 chr16 90354753 256040 0.002833719217847898 0.7096043386297961 chr17 81195210 845551 0.010413803967007413 2.487736012596467 chr18 78077248 225638 0.002889932800910196 0.8205357540037129 chr19 59128983 142900 0.0024167505130267505 0.5572250497369039 chr20 63025520 330458 0.005243241150568849 1.6917655038249553 chr21 48129895 95383 0.0019817828399584085 0.3716038696441312 chr22 51304566 148350 0.0028915555001478815 0.7113967562631469 chrMT 16571 817261 49.31874962283507 213.20445634792833 chrX 155270560 27146057 0.17483067620803325 8.558293104839999 chrY 59373566 732965 0.012344971834772397 1.908970130641967