BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006086.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 = 5,528,842 number of mapped reads = 4,746,674 (85.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,399,372 number of mapped paired reads (second in pair) = 2,347,302 number of mapped paired reads (both in pair) = 4,368,210 number of mapped paired reads (singletons) = 378,464 number of mapped bases = 183,313,895 bp number of sequenced bases = 183,293,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 200,909 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 63,503.4316 std insert size = 2,474,500.9393 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 46.9829 >>>>>>> ACTG content number of A's = 48,457,925 bp (26.44%) number of C's = 41,112,901 bp (22.43%) number of T's = 50,147,333 bp (27.36%) number of G's = 43,568,053 bp (23.77%) number of N's = 7,632 bp (0%) GC percentage = 46.2% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 931,652 number of insertions = 5,956 mapped reads with insertion percentage = 0.13% number of deletions = 15,565 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.08% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.3536X There is a 4.2% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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% 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 15627772 0.06269902934364203 0.3671016318543588 chr2 243199373 15837697 0.06512227726837108 0.39481709875756776 chr3 198022430 12538538 0.06331877656485682 0.3351309140755593 chr4 191154276 11077392 0.05795000892368215 0.33173965745634815 chr5 180915260 10984116 0.06071414871249667 0.32830608861658184 chr6 171115067 10494526 0.06133022757136869 0.3472689248778182 chr7 159138663 9959608 0.06258446446794642 0.41020500424167966 chr8 146364022 9127030 0.0623584257612161 0.38096037559059476 chr9 141213431 7770925 0.05502964516172686 0.33059153201361735 chr10 135534747 8960967 0.06611564339290794 0.3560724761896504 chr11 135006516 8540450 0.06325953926549738 0.4261310559910065 chr12 133851895 8390997 0.06268866794900438 0.3353178870429985 chr13 115169878 5639767 0.04896911499723912 0.29855315280366784 chr14 107349540 5832147 0.05432857001529769 0.31660880813360237 chr15 102531392 5580617 0.05442837448261699 0.3161149787581688 chr16 90354753 5962624 0.06599126002812492 0.40249937293749877 chr17 81195210 5655639 0.06965483555002813 0.3707517823025345 chr18 78077248 4692548 0.06010134988364344 0.37608792601675833 chr19 59128983 4342841 0.07344690843067604 0.41688727383352164 chr20 63025520 4452515 0.07064622394230147 0.3692188265431331 chr21 48129895 2472053 0.051362110804521806 0.3441387506462349 chr22 51304566 2711917 0.05285917436666358 0.35079438234141297 chrMT 16571 19962 1.2046346026190333 1.7869500289318414 chrX 155270560 5456596 0.03514250222321604 0.2511152313507479 chrY 59373566 1184651 0.019952498726453452 0.2160624339711014