jpHMM-HIV [Result]

Input data:

• sequence file

jpHMM result:

Sequence #1: >BF1_AX032749_EU446022

This sequence is related to subtype(s): B F1

Fragment Start Position	Uncertainty Region Start - End	Breakpoint Interval Start - End	Fragment End Position	Fragment Subtype
Position in the original sequence [pred_recombination], [recombination_incl_UR_and_BPI], [UR_and_BPI]
1	-	-	789	N/A
790	-	1501 - 1530	1530	B
1531	-	1750 - 1832	1808	F1
1809	3287 - 3589	5077 - 5116	5095	B
5096	-	5368 - 5404	5397	F1
5398	-	6883 - 6918	6899	B
6900	-	7153 - 7171	7165	F1
7166	-	-	8060	B
Position based on HXB2 numbering [pred_recombination] [recombination_incl_UR_and_BPI] [UR_and_BPI]
1	-	-	789	N/A
790	-	1501 - 1530	1530	B
1531	-	1750 - 1832	1808	F1
1809	3287 - 3589	5077 - 5116	5095	B
5096	-	5368 - 5404	5397	F1
5398	-	6893 - 6928	6909	B
6910	-	7169 - 7184	7178	F1
7179	-	-	8073	B
Genome map (based on HXB2 numbering)
Note: Numbers in the above figure denote intervals for recombination breakpoints based on HXB2 numbering. The uncolored regions denote missing information due to input fragment sequence. The gray regions denote missing infomation due to uninformative subtype models (subtype: N/A). The sequence regions of less than 10 nucleotides long are too short to be mapped onto the genome map.
Posterior probabilities of the subtypes (based on HXB2 numbering)

Posterior probabilities of the subtypes at each sequence position (original sequence positions) calculated by jpHMM: [text]

Alignment of the query sequences to the HXB2 sequence determined by jpHMM: query_to_ref_alignments.txt

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