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Table 2 Haplotypes identified by BAsE-Seq in Lib_1:9 and Lib_1:99

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

Haplotypes a

Lib_1:9

Lib_1:99

Individual b

Bulk c

Individual b

Bulk c

........................................................

2,118

88.6%

85.7%

3,656

99.5%

99.3%

ACACTAAATTTAAACAG

270

11.3%

14.3%

14

0.4%

0.7%

....C................................................

1

0.04%

0%

1

0.03%

0%

ACACTAAATTTAAA...AG

1

0.04%

0%

0

0%

0%

....................A................................

0

0%

0%

2

0.05%

0%

Total

2,390

100%

100%

3,673

100%

100%

  1. aHaplotypes observed in individual genomes. The major allele (Clone-2) is represented by a period and the minor allele (Clone-1) is represented by the base at that position (Table S2 in Additional file 2).
  2. bHaplotype frequencies observed in individual genomes.
  3. cAverage allele frequency of SNPs from 'bulk' analysis.
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Genome Biology

ISSN: 1474-760X

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