BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006026.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 = 12,354,842 number of mapped reads = 8,263,403 (66.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,186,436 number of mapped paired reads (second in pair) = 4,076,967 number of mapped paired reads (both in pair) = 7,189,276 number of mapped paired reads (singletons) = 1,074,127 number of mapped bases = 319,087,400 bp number of sequenced bases = 319,052,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 262,142 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 69,878.684 std insert size = 2,563,100.9924 median insert size = 97 >>>>>>> Mapping quality mean mapping quality = 47.0847 >>>>>>> ACTG content number of A's = 95,025,112 bp (29.78%) number of C's = 64,821,336 bp (20.32%) number of T's = 93,466,051 bp (29.29%) number of G's = 65,619,156 bp (20.57%) number of N's = 121,047 bp (0.04%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 2,267,097 number of insertions = 8,978 mapped reads with insertion percentage = 0.11% number of deletions = 27,435 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.48% >>>>>>> Coverage mean coverageData = 0.1031X std coverageData = 0.5917X There is a 7.76% of reference with a coverageData >= 1X There is a 1.81% 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 24935993 0.10004385505623274 0.8407417220515857 chr2 243199373 27361493 0.11250642903590051 0.54100610742703 chr3 198022430 22024603 0.11122276905702046 0.41533915840834934 chr4 191154276 22896519 0.11978031294471278 0.4913698215251657 chr5 180915260 20932029 0.11570073746128436 0.4255713068585301 chr6 171115067 18996748 0.11101738925187693 0.5476709111152294 chr7 159138663 17530750 0.11016021920455622 0.6869942437668123 chr8 146364022 16771466 0.11458735398785365 1.3199056184315552 chr9 141213431 13692925 0.09696616605824131 0.4619449541884769 chr10 135534747 14270400 0.10528960518146686 0.6289648910317129 chr11 135006516 14694298 0.1088413984403538 0.47709061639893935 chr12 133851895 13879949 0.10369632047420771 0.40277954243306563 chr13 115169878 10417106 0.09044991781618454 0.3732112473726434 chr14 107349540 9725915 0.09060043480391253 0.41068147086164164 chr15 102531392 8435043 0.0822679067889764 0.3567214068884593 chr16 90354753 8291355 0.09176445869980963 0.4455930031457835 chr17 81195210 7317853 0.09012665894946266 0.39464540229265044 chr18 78077248 8667663 0.11101394096267328 0.6917272183516416 chr19 59128983 5455431 0.09226323070701216 0.6577235014360925 chr20 63025520 6281569 0.09966707137045439 0.4144448633086252 chr21 48129895 4095157 0.08508551701598352 0.418989464084028 chr22 51304566 3002523 0.05852350451614775 0.30157118083151885 chrMT 16571 45712 2.758554100537083 2.7303872227063986 chrX 155270560 18528842 0.1193326152749111 0.4736594810086795 chrY 59373566 836058 0.014081316928142736 0.29489227471768065