BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006053.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 = 6,271,448 number of mapped reads = 5,502,993 (87.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,795,295 number of mapped paired reads (second in pair) = 2,707,698 number of mapped paired reads (both in pair) = 5,065,218 number of mapped paired reads (singletons) = 437,775 number of mapped bases = 212,531,362 bp number of sequenced bases = 212,508,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 247,127 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 56,052.0442 std insert size = 2,316,082.364 median insert size = 94 >>>>>>> Mapping quality mean mapping quality = 46.8648 >>>>>>> ACTG content number of A's = 56,270,870 bp (26.48%) number of C's = 47,786,680 bp (22.49%) number of T's = 58,205,448 bp (27.39%) number of G's = 50,235,169 bp (23.64%) number of N's = 10,079 bp (0%) GC percentage = 46.13% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 983,786 number of insertions = 6,965 mapped reads with insertion percentage = 0.13% number of deletions = 18,055 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0687X std coverageData = 0.4014X There is a 4.7% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% 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% 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 18274632 0.0733183007796799 0.42501618491531784 chr2 243199373 18410628 0.07570179056341564 0.45385569614511334 chr3 198022430 14426337 0.07285203499421758 0.36763288866784066 chr4 191154276 12708357 0.0664822010050144 0.3648206559213942 chr5 180915260 12680713 0.07009200329480222 0.36076250325048204 chr6 171115067 12118080 0.07081831081537665 0.3957238105433487 chr7 159138663 11542896 0.0725335740693008 0.478798184148984 chr8 146364022 10543427 0.07203564684769322 0.41417422296031575 chr9 141213431 9038145 0.06400343746339539 0.36876133499776226 chr10 135534747 10275957 0.07581787864332679 0.39185730434707755 chr11 135006516 9968480 0.07383702872533945 0.5529475259061233 chr12 133851895 9785536 0.07310719060047674 0.3703742725300588 chr13 115169878 6485227 0.05631009698560243 0.32587046284763344 chr14 107349540 6668280 0.0621174529485641 0.34822920563615306 chr15 102531392 6512287 0.06351505497945449 0.3482810318751616 chr16 90354753 7001598 0.07749009064304564 0.4390960849229255 chr17 81195210 6733386 0.08292836486290263 0.4304298120629648 chr18 78077248 5389805 0.06903169794099301 0.43917119263498666 chr19 59128983 5070528 0.08575368191264172 0.4852775833472921 chr20 63025520 5203536 0.08256236521332946 0.4059478878160377 chr21 48129895 2851495 0.059245818009783735 0.380387292231566 chr22 51304566 3143046 0.06126250049556993 0.3840197795796018 chrMT 16571 24104 1.4545893428278318 2.2083333707794335 chrX 155270560 6305504 0.040609784623691705 0.27919998751256836 chrY 59373566 1369378 0.02306376544740466 0.23756508880024163