BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472388.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,438,998 number of mapped reads = 17,271,569 (99.04%) number of supplementary alignments = 68,486 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,659,304 number of mapped paired reads (second in pair) = 8,612,265 number of mapped paired reads (both in pair) = 17,172,848 number of mapped paired reads (singletons) = 98,721 number of mapped bases = 1,695,172,299 bp number of sequenced bases = 1,694,944,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,706,501 duplication rate = 47.32% >>>>>>> Insert size mean insert size = 17,885.7913 std insert size = 1,312,898.9734 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.7679 >>>>>>> ACTG content number of A's = 455,387,586 bp (26.87%) number of C's = 393,492,860 bp (23.22%) number of T's = 456,088,752 bp (26.91%) number of G's = 389,761,075 bp (23%) number of N's = 213,956 bp (0.01%) GC percentage = 46.21% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,521,979 number of insertions = 97,938 mapped reads with insertion percentage = 0.56% number of deletions = 79,167 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.5476X std coverageData = 17.1403X There is a 4.63% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 170029729 0.6821637126432676 20.397386271363636 chr2 243199373 127934595 0.5260482106588326 15.724266723243002 chr3 198022430 135214089 0.6828220873766674 16.829188472992367 chr4 191154276 46306881 0.24224873211834402 9.783394158570584 chr5 180915260 61058652 0.33749862781061146 11.827231935112147 chr6 171115067 131160606 0.7665053013712697 17.87940785779803 chr7 159138663 113972410 0.7161830308955153 19.103410326389103 chr8 146364022 72639445 0.49629303709623396 13.071647805836129 chr9 141213431 56828960 0.4024331085050968 11.0646615502919 chr10 135534747 43355317 0.3198834096764869 9.636190388370965 chr11 135006516 52698783 0.3903425150234971 18.876832779380432 chr12 133851895 84688277 0.6327013674330124 16.411193250765688 chr13 115169878 53831919 0.46741318072768995 21.772881949883548 chr14 107349540 40637451 0.37855263282916723 10.69336757275012 chr15 102531392 29284645 0.2856163798107803 12.314623396229873 chr16 90354753 81405548 0.9009547953719712 24.743360690484952 chr17 81195210 80228872 0.9880985836479763 26.373079762088974 chr18 78077248 17935478 0.22971452579886012 7.554524585603666 chr19 59128983 53391282 0.9029629682621126 19.589796006451778 chr20 63025520 54783177 0.8692221341450257 23.18047757349154 chr21 48129895 12647206 0.2627723580115851 13.657711902184754 chr22 51304566 17184020 0.3349413383596306 8.314406415742834 chrMT 16571 41332 2.494236919920343 2.052508036125969 chrX 155270560 157589860 1.0149371522843738 28.50998036171799 chrY 59373566 323765 0.005453015909470555 0.37383359245537634