BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008796.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,749,772 number of mapped reads = 1,488,096 (85.05%) number of supplementary alignments = 7,219 (0.41%) number of secondary alignments = 0 number of mapped bases = 96,300,363 bp number of sequenced bases = 96,252,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,033 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7957 >>>>>>> ACTG content number of A's = 25,674,459 bp (26.67%) number of C's = 17,417,334 bp (18.1%) number of T's = 30,764,356 bp (31.96%) number of G's = 22,361,471 bp (23.23%) number of N's = 34,417 bp (0.04%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 781,368 number of insertions = 6,183 mapped reads with insertion percentage = 0.41% number of deletions = 27,816 mapped reads with deletion percentage = 1.85% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.301X There is a 2.67% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 7924998 0.031795298917229174 0.5734417937310194 chr2 243199373 9020001 0.037088915521176116 0.3485245098908107 chr3 198022430 8921919 0.04505509300133323 0.2467823333107456 chr4 191154276 3297960 0.017252870660345573 0.16038216794520752 chr5 180915260 4113884 0.022739286890448046 0.17129676801466495 chr6 171115067 5742740 0.0335606916485034 0.2461262045789624 chr7 159138663 4553182 0.028611412928610566 0.25095634253001886 chr8 146364022 7345219 0.05018459386146139 0.3063753697895376 chr9 141213431 3562929 0.02523080825081008 0.2756581940744726 chr10 135534747 6447397 0.04757006703233083 0.4099089549812274 chr11 135006516 4837111 0.03582872251884494 0.31347888199277435 chr12 133851895 3597555 0.026877131623724865 0.18843845476914656 chr13 115169878 2009057 0.017444292161184715 0.14652265098332298 chr14 107349540 3684009 0.03431788343014791 0.2126549734383256 chr15 102531392 2346682 0.02288744894831819 0.16939657354698015 chr16 90354753 2455864 0.027180241420171888 0.21734186734558164 chr17 81195210 2758177 0.03396970092201252 0.28012126025262557 chr18 78077248 1692677 0.021679516675587745 0.4369876812579624 chr19 59128983 1780885 0.03011864756747127 0.38425560340209863 chr20 63025520 2168027 0.03439919258103701 0.21177654441415225 chr21 48129895 983668 0.020437775731694408 0.1746401664175587 chr22 51304566 1110138 0.021638191033523217 0.16329262878803213 chrMT 16571 6321 0.38144952024621326 0.6486501060659734 chrX 155270560 5651198 0.03639581128579687 0.24518767077151474 chrY 59373566 288765 0.004863527988195959 0.14566912548291935