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Table 4 Recombination analysis of 21 ASGV genomes using RDP4 program

From: Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

  In alignment In recombinant sequence Relative to CTLV_Lily     Detection methods
Begin End Begin End Begin End Recombinant sequence(s) Minor parental sequence(s) Major parental sequence(s) RDP GENECONV Bootscan Maxchi Chimaera SiSscan PhylPro LARD 3Seq
1 6492 1926 6487 1924 6488 1925 ASGV_YTG Unknown (ASGV_HH), Unknown (ASGV_CHN) ASGV_Fuji 1.30E-31 3.39E-09 8.78E-30 1.16E-10 9.12E-16 9.16E-27 NS NS 3.17E-17
2 6492 2488 6488 2487 6488 2487 ASGV_HH, ASGV_CHN, CTLV_MTH[P] ASGV_Fuji, CTLV_MTH ASGV_Li-23, CTLV_Lily 3.40E-19 3.89E-04 1.47E-16 1.29E-16 1.83E-10 1.06E-27 NS NS 1.48E-13
3 4112 4552 4110 4550 4110 4550 PBNLSV ASGV_Li-23, CTLV_Lily ASGV_KFP 1.20E-12 2.22E-08 8.19E-11 2.20E-05 2.75E-05 1.41E-10 NS NS NS
4 5844 6224 5842 6221 5842 6221 PBNLSV ASGV_Li-23, CTLV_Lily Unknown (CTLV_Pk), Unknown (CTLV_Kumquat1), Unknown (CTLV_LCd-NA-1), Unknown (CTLV_SO), Unknown (CTLV_XHC), Unknown (ASGV_Matsuco) 6.90E-07 1.12E-08 1.61E-07 6.45E-04 6.44E-04 1.30E-06 NS NS NS
5 5819 6412a 5816 6408a 5817 6409a ASGV_YTG ASGV_HH, ASGV_CHN ASGV_P-209, ASGV_T47 2.42E-08 2.14E-03 1.58E-09 2.89E-03 1.65E-02 1.97E-07 NS NS NS
6 4412 4946 4409 4943 4410 4944 CTLV_LCd-NA-1 CTLV_SO, CTLV_Kumquat1, CTLV_XHC Unknown (ASGV_Matsuco) 1.20E-02 2.91E-04 1.01E-02 4.02E-04 5.76E-03 4.04E-03 NS NS NS
  1. Minor Parent Parent contributing smaller fraction of sequence, Major Parent Parent contributing larger fraction of sequence, Unknown Only one parent and a recombinant need be in the alignment for a recombination event to be detectable. The sequence listed as unknown was used to infer the existence of a missing parental sequence, NS No significant P-value was recorded for this recombination event using this method
  2. aThe actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event)