BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549115.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,044,333 number of mapped reads = 5,361,907 (59.28%) number of secondary alignments = 0 number of mapped bases = 212,879,876 bp number of sequenced bases = 212,859,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,415 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3338 >>>>>>> ACTG content number of A's = 61,680,137 bp (28.98%) number of C's = 44,651,746 bp (20.98%) number of T's = 61,906,574 bp (29.08%) number of G's = 44,612,783 bp (20.96%) number of N's = 8,600 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 644,526 number of insertions = 5,420 mapped reads with insertion percentage = 0.1% number of deletions = 16,039 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.0688X std coverageData = 0.4346X There is a 5.84% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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% 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 17366137 0.06967339511663644 0.7464098180542937 chr2 243199373 18308705 0.0752826982000484 0.42932516517416996 chr3 198022430 14606035 0.07375949785082428 0.3101279473476399 chr4 191154276 13488592 0.07056390410016253 0.3098800551742553 chr5 180915260 13156616 0.07272253319040085 0.3131790566279737 chr6 171115067 12601269 0.07364207735137666 0.3424152979471531 chr7 159138663 13159835 0.08269414076955013 0.6607591968325224 chr8 146364022 10871683 0.07427838379571176 0.4198332021118058 chr9 141213431 9076044 0.0642718184504702 0.40685223279110777 chr10 135534747 10168857 0.07502767537537809 0.3989781056700773 chr11 135006516 9919561 0.07347468325158468 0.4041497071281244 chr12 133851895 9736890 0.07274375906295537 0.317359483763655 chr13 115169878 6782712 0.058893107449501686 0.27443132709527746 chr14 107349540 6673696 0.06216790495795324 0.34007709320593144 chr15 102531392 6371088 0.06213792552431162 0.2832831998224968 chr16 90354753 6262256 0.06930743311312024 0.32781242932200055 chr17 81195210 5799958 0.07143226798723717 0.32269074138133336 chr18 78077248 5727598 0.07335809274425246 0.7847214414872228 chr19 59128983 4257925 0.07201079375912825 0.6210064192684925 chr20 63025520 4630059 0.07346324155675352 0.32252856043086453 chr21 48129895 2766694 0.057483898520867334 0.30367151341590365 chr22 51304566 2561508 0.049927485986335014 0.26553805240010336 chrMT 16571 58523 3.531651680646913 5.250011999148469 chrX 155270560 6922410 0.04458288808902344 0.28848607710402147 chrY 59373566 1605225 0.027036021383657502 0.22795667081409665