BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006192.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 = 7,033,628 number of mapped reads = 6,054,922 (86.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,053,468 number of mapped paired reads (second in pair) = 3,001,454 number of mapped paired reads (both in pair) = 5,566,460 number of mapped paired reads (singletons) = 488,462 number of mapped bases = 234,317,603 bp number of sequenced bases = 234,281,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,927 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 53,099.3088 std insert size = 2,184,281.4964 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 47.8573 >>>>>>> ACTG content number of A's = 65,321,295 bp (27.88%) number of C's = 50,216,635 bp (21.43%) number of T's = 66,546,101 bp (28.4%) number of G's = 52,170,296 bp (22.27%) number of N's = 27,630 bp (0.01%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 749,325 number of insertions = 6,788 mapped reads with insertion percentage = 0.11% number of deletions = 25,961 mapped reads with deletion percentage = 0.43% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0757X std coverageData = 0.5279X There is a 5.48% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% 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 19512804 0.07828587917540233 0.6133100881221921 chr2 243199373 20247908 0.08325641530334044 0.4343716913030468 chr3 198022430 15716621 0.0793678827191445 0.3688233799896148 chr4 191154276 15353313 0.08031896184210914 0.38602594727899947 chr5 180915260 14806860 0.081844173896663 0.3750615934973917 chr6 171115067 14147192 0.08267648342153296 0.41548362386968263 chr7 159138663 12365667 0.07770372558678591 0.5215883769704087 chr8 146364022 11620971 0.0793977293135604 1.0176625562389041 chr9 141213431 9659402 0.0684028560994315 0.38462015944635763 chr10 135534747 11225975 0.08282728413548446 0.43745547576593263 chr11 135006516 10879591 0.08058567336112873 0.4658920489572312 chr12 133851895 10932824 0.08167851489887386 0.37984991347828795 chr13 115169878 7675125 0.06664177416251149 0.33806321584726684 chr14 107349540 6524788 0.060780772791387834 1.3112286816441836 chr15 102531392 6964092 0.0679215590869965 0.3443272035407381 chr16 90354753 6952599 0.0769477948769336 0.38857406477509043 chr17 81195210 6005707 0.07396627214832008 0.3802973705720528 chr18 78077248 6363799 0.08150644602637634 0.5742797171214505 chr19 59128983 4232784 0.07158560464332694 0.4860995540626037 chr20 63025520 5035116 0.07989011435367768 0.3992307398458258 chr21 48129895 3058085 0.06353816063799848 0.35803377088607463 chr22 51304566 2701557 0.05265724302199535 0.32745682838428636 chrMT 16571 15962 0.9632490495443847 1.7354204641834323 chrX 155270560 11844937 0.0762857878531513 0.38839882980603474 chrY 59373566 473924 0.007982070674346897 0.1635940464879431