Fig 1.
Schematic summary of the analysis in this study.
The methodology adopted in the sampling, library preparation, sequencing and analysis involving custom based pipeline and COVIDSeq pipeline employed in this study.
Fig 2.
Concordance among replicate samples considered in the analysis.
A) Total number of read counts B) The coverage percentage among replicates. R1-Replicate 1, and R2- Replicate 2.
Fig 3.
The line plot for the mean coverage of SARS-CoV-2 genome.
The mean coverage for the 98 amplicons across the SARS-CoV-2 genome.
Fig 4.
Variant number per genome and their annotation.
(A) Distribution of variants in the genomes with ≥ 99% coverage (B) Summary of the variant annotations.
Fig 5.
Phylogenetic distribution of Indian SARS-CoV-2 genomes.
A) Phylogenetic trees generated by Nextstrain. 469 COVIDseq genomes reported from this study are highlighted. The 469 genomes cluster under clade A2a, I/A3i and B4, with A2a being the dominant clade. B) The proportion of clades and PANGOLIN lineages representing the Indian genomes. B.1 and B.1.113 are the dominant lineages in COVIDseq genomes whereas other Indian genomes show a dominance of B.6 and B.1 lineages.
Fig 6.
Phylogenetic distribution of PANGOLIN lineages in COVIDseq genomes.
The distribution of lineages assigned by PANGOLIN in 469 COVIDseq genomes with the Wuhan/WH01 (EPI_ISL_406798) as reference.
Fig 7.
The coverage plot across the SARS-CoV-2 genome.
The coverage plot constructed using Integrative Genome Viewer (IGV) for samples that were negative on RT-PCR assays but detected by DRAGEN COVIDSeq Pipeline.