BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006018.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 11,735,334 number of mapped reads = 8,537,642 (72.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,321,166 number of mapped paired reads (second in pair) = 4,216,476 number of mapped paired reads (both in pair) = 7,591,532 number of mapped paired reads (singletons) = 946,110 number of mapped bases = 330,008,519 bp number of sequenced bases = 329,972,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,033 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 69,559.0715 std insert size = 2,573,613.2666 median insert size = 111 >>>>>>> Mapping quality mean mapping quality = 47.438 >>>>>>> ACTG content number of A's = 95,247,640 bp (28.87%) number of C's = 69,313,960 bp (21.01%) number of T's = 94,782,853 bp (28.72%) number of G's = 70,371,932 bp (21.33%) number of N's = 255,692 bp (0.08%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,195,963 number of insertions = 9,053 mapped reads with insertion percentage = 0.11% number of deletions = 28,071 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.76% >>>>>>> Coverage mean coverageData = 0.1066X std coverageData = 0.6079X There is a 8.09% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 27194967 0.10910691773161119 0.8556787764012703 chr2 243199373 28525834 0.1172940277276126 0.5142139303465924 chr3 198022430 22805036 0.11516390340225599 0.41842079124006504 chr4 191154276 22279290 0.11655135561811863 0.4971371719284985 chr5 180915260 20583872 0.1137763171553356 0.41781026093928963 chr6 171115067 19357308 0.11312450936889151 0.5086865760541301 chr7 159138663 17946738 0.11277421628206089 0.651887772647534 chr8 146364022 17030544 0.11635744746068812 1.5070460645168626 chr9 141213431 13802837 0.09774450562000721 0.4411243450522876 chr10 135534747 15076088 0.11123411769824604 0.6395813744633697 chr11 135006516 13823433 0.10239085793459035 0.4334349186429063 chr12 133851895 15424745 0.11523740474499819 0.42637990939749687 chr13 115169878 10667793 0.09262658939345234 0.3759868294454553 chr14 107349540 10062079 0.09373192470130752 0.39419348330629084 chr15 102531392 9247247 0.09018942218203767 0.3708113748584113 chr16 90354753 9337982 0.10334798878814931 0.4725239659896432 chr17 81195210 8165053 0.1005607719962791 0.408690768268721 chr18 78077248 8337099 0.10678013395144255 0.6237003841813142 chr19 59128983 6377549 0.10785825624634876 0.7139601491851514 chr20 63025520 6792090 0.10776729807227295 0.4297949313803183 chr21 48129895 4592090 0.09541034735272122 0.42683509989411633 chr22 51304566 3566351 0.06951332557807818 0.34545194657911654 chrMT 16571 53544 3.2311870134572445 2.64114188213884 chrX 155270560 18104671 0.11660079669964481 0.44822751431840097 chrY 59373566 854279 0.01438820433995829 0.33241889255513324