jpHMM-HBV [Result]

Input data:

• sequence file

jpHMM result:

Sequence #1: D00330

This sequence is related to genotype(s): B C

Fragment Start Position	Uncertainty Region Start - End	Breakpoint Interval Start - End	Fragment End Position	Fragment Genotype
Position in the original sequence [pred_recombination], [recombination_incl_UR_and_BPI], [UR_and_BPI]
1	-	1759 - 1981	1837	B
1838	-	2199 - 2287	2232	C
2233	-	-	3215	B
Position based on reference genome AM282986 numbering [pred_recombination] [recombination_incl_UR_and_BPI] [UR_and_BPI]
1	-	1759 - 1981	1837	B
1838	-	2199 - 2287	2232	C
2233	-	-	3221	B
Genome map (with position numbers given relative to the HBV reference genome AM282986; the sequence has an offset of 0 to the reference origin (see pairwise alignment to reference sequence)):
Note: The predicted genotype recombination is represented in the outer ring. In the second inner ring, the posterior probabilities for each genotype are plotted. Regions with a shading of two colors mark breakpoint intervals, with a shading of gray color uncertainty regions. Gray regions denote missing infomation due to uninformative genotype models or input fragment sequence (genotype: N/A) Positions of genes in the HBV reference genome AM282986 are marked with grey and black bars in the inner ring.

Posterior probabilities of the genotypes at each sequence position calculated by jpHMM: [text]

Pairwise alignment of each query sequence to the reference genome AM282986 determined by jpHMM: query_to_ref_alignments.txt
(Numbers x and y given in the output (">AM282986 x y") indicate the start (x) and end (y) position in the reference genome. Negative numbers x indicate an offset of x to the reference origin.)

The circular figures were plotted using the software package Circos (Krzywinski et al., Genome Res (2009)).

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