BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153321.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 59,968,462 number of mapped reads = 59,484,837 (99.19%) number of supplementary alignments = 479,210 (0.8%) number of secondary alignments = 0 number of mapped bases = 5,762,255,700 bp number of sequenced bases = 5,761,280,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,743,398 duplication rate = 36.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1817 >>>>>>> ACTG content number of A's = 1,548,230,208 bp (26.87%) number of C's = 1,325,214,278 bp (23%) number of T's = 1,581,106,919 bp (27.44%) number of G's = 1,305,142,112 bp (22.65%) number of N's = 1,587,184 bp (0.03%) GC percentage = 45.66% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 16,442,854 number of insertions = 601,646 mapped reads with insertion percentage = 1% number of deletions = 469,322 mapped reads with deletion percentage = 0.78% homopolymer indels = 49.49% >>>>>>> Coverage mean coverageData = 1.8614X std coverageData = 19.1671X There is a 22.82% of reference with a coverageData >= 1X There is a 12.31% of reference with a coverageData >= 2X There is a 6.93% of reference with a coverageData >= 3X There is a 5.07% of reference with a coverageData >= 4X There is a 3.93% of reference with a coverageData >= 5X There is a 3.35% of reference with a coverageData >= 6X There is a 2.96% of reference with a coverageData >= 7X There is a 2.69% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.21% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 2% of reference with a coverageData >= 13X There is a 1.91% of reference with a coverageData >= 14X There is a 1.83% of reference with a coverageData >= 15X There is a 1.76% of reference with a coverageData >= 16X There is a 1.69% of reference with a coverageData >= 17X There is a 1.63% of reference with a coverageData >= 18X There is a 1.58% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.48% of reference with a coverageData >= 21X There is a 1.43% of reference with a coverageData >= 22X There is a 1.39% of reference with a coverageData >= 23X There is a 1.35% of reference with a coverageData >= 24X There is a 1.31% of reference with a coverageData >= 25X There is a 1.27% of reference with a coverageData >= 26X There is a 1.24% of reference with a coverageData >= 27X There is a 1.21% of reference with a coverageData >= 28X There is a 1.18% of reference with a coverageData >= 29X There is a 1.15% of reference with a coverageData >= 30X There is a 1.12% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 1.06% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 1.02% of reference with a coverageData >= 35X There is a 0.99% of reference with a coverageData >= 36X There is a 0.97% of reference with a coverageData >= 37X There is a 0.95% of reference with a coverageData >= 38X There is a 0.93% of reference with a coverageData >= 39X There is a 0.91% of reference with a coverageData >= 40X There is a 0.89% of reference with a coverageData >= 41X There is a 0.87% of reference with a coverageData >= 42X There is a 0.86% of reference with a coverageData >= 43X There is a 0.84% of reference with a coverageData >= 44X There is a 0.82% of reference with a coverageData >= 45X There is a 0.81% of reference with a coverageData >= 46X There is a 0.79% of reference with a coverageData >= 47X There is a 0.78% of reference with a coverageData >= 48X There is a 0.76% of reference with a coverageData >= 49X There is a 0.75% of reference with a coverageData >= 50X There is a 0.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 691213727 2.7731675220179293 28.87171317675941 chr2 243199373 364284549 1.497884408608241 13.236493227845783 chr3 198022430 328452393 1.6586625717096795 14.920179872831 chr4 191154276 252001669 1.3183156258560493 13.33830697533654 chr5 180915260 308723843 1.7064555140345816 16.06261770325434 chr6 171115067 184095419 1.075857446264507 11.959213883588461 chr7 159138663 295662313 1.857891146163519 18.038743923248532 chr8 146364022 352535573 2.4086217923145075 26.15647847108204 chr9 141213431 114742928 0.8125496787908226 8.979126798838678 chr10 135534747 302380544 2.231018618421149 18.550889475704935 chr11 135006516 255034210 1.8890511180956628 16.447153666949788 chr12 133851895 283843553 2.1205792641187484 18.080813774380772 chr13 115169878 70654753 0.6134829195529755 7.220200922186999 chr14 107349540 161369565 1.5032161758681033 14.184049499196876 chr15 102531392 229793140 2.2411978957625 20.27746794757796 chr16 90354753 249722776 2.763803427142344 23.76468580127493 chr17 81195210 203004926 2.5002081526730455 17.965182102489056 chr18 78077248 65264040 0.8358906297517044 10.602240668607134 chr19 59128983 350612237 5.929617240330347 48.34158251129363 chr20 63025520 121411935 1.9263932292823605 16.63323396044237 chr21 48129895 60243044 1.2516761983378522 12.312969874183686 chr22 51304566 69754360 1.3596130995436158 13.554660555551711 chrMT 16571 9456 0.5706354474684691 1.864488760973021 chrX 155270560 443170995 2.8541855906232323 27.384697980091357 chrY 59373566 4273752 0.07198071950066129 2.914649367006006