BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

Table 3 Comparison of haplotypes observed over a 367 bp region in S7.1

SNV position ^a	118	119	192	258	484
Consensus base ^b	T	G	C	G	C
Variant base	G	A	T	C	A
Deep-Seq frequency (%)	19.6	45.2	46.7	47.3	4.5
BAsE-Seq frequency (%)	18.5	61.5	39.9	40.6	4.2
						Observed in clones	Observed in BAsE-Seq
Haplotypes ^c	.	A	.	.	.	10 (50%)	1,588 (62%)
	.	.	T	C	.	2 (10%)	428 (17%)
	G	.	T	C	.	5 (25%)	403 (16%)
	.	.	T	C	A	0	65 (3%)
	G	.	T	C	A	0	27 (1%)
	.	.	.	.	.	0	24 (1%)
	G	A	T	C	.	0	14 (0.5%)
	.	A	.	.	A	1 (5%)	2 (0.08%)
	.	.	T	.	.	0	2 (0.08%)
	G	.	.	C	.	0	2 (0.08%)
	.	A	T	C	.	2 (10%)	0
Unique haplotypes						5	10
Total observed haplotypes						20	2,555

^aSNVs identified by all three methods - Sanger sequencing of clones, Deep-Seq and BAsE-Seq.
^bBase call in the bulk consensus genome.
^cA period on the haplotype indicates that the position carries the consensus base. SNVs are represented by the identity of the variant base.

ISSN: 1474-760X