Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

Table 2 Haplotype reconstruction of quasispecies datasets

Dataset		No. of haplotypes		Mean Hamming	MHD of top 4	MHD of
		reconstructed		distance (MHD)	haplotypes	top 4: pruned
	Mode	Min	Max
LQ4_1 to LQ4_100	6	5	8	75.76	13.63	4.94

Haplotype reconstructions from populations having a simulated viral quasispecies structure. Nine quasispecies were present in each simulated population and the diversity between them was 4% (see Methods). The pruned haplotype genomes were created by excluding the initial and final 50 bp from the reconstructed haplotypes to avoid errors due to low read coverage. A 100 simulations were performed.

ISSN: 1742-4690