S1 Table -

(A) Genome sequencing statistics for each sample sequenced in this study. Legend: SRA (Sequence Read Archive), QF (quality-filtered). (B) Categorized number of MVs for each sample sequenced in this study. Legend: NCR (non-coding region), CR (coding region). (C) List of detected MVs from deep sequencing of HSV-1 original stock and plaque-purified clones 1–5. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (D) List of detected MVs from deep sequencing of HSV-2 original stock and plaque-purified clones 1–5. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (E) List of detected MVs from ultra-deep sequencing of HSV-1 plaque-purified clones 2 and 3. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (F) List of detected MVs from ultra-deep sequencing of HSV-2 plaque-purified clones 1 and 5. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (G) List of detected MVs from ultra-deep sequencing of HSV-1 clone 2 at P0, P5, and P10 in Vero cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (H) List of detected MVs from ultra-deep sequencing of HSV-1 clone 2 at P0 in Vero cells, and P5 and P10 in HaCaT cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (I) List of detected MVs from ultra-deep sequencing of HSV-1 clone 3 at P0, P5, and P10 in Vero cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (J) List of detected MVs from ultra-deep sequencing of HSV-1 clone 3 at P0 in Vero cells, and P5 and P10 in HaCaT cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (K) List of detected MVs from ultra-deep sequencing of HSV-2 clone 1 at P0, P5, and P10 in Vero cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (L) List of detected MVs from ultra-deep sequencing of HSV-2 clone 1 at P0 in Vero cells, and P5 and P10 in HaCaT cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (M) List of detected MVs from ultra-deep sequencing of HSV-2 clone 5 at P0, P5, and P10 in Vero cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (N) List of detected MVs from ultra-deep sequencing of HSV-2 clone 5 at P0 in Vero cells, and P5 and P10 in HaCaT cells. Legend: Ref (reference allele), Var (variant allele), NCR (non-coding region), INS (insertion), DEL (deletion), name_freq (variant allele frequency), name_cov (total coverage), name_Ref (reference allele coverage), name_Var (variant allele coverage). (O) List of total MVs detected from variant analysis performed with four different variant calling tool sets, for each sample sequenced in this study. (P) List of de novo MVs detected from variant analysis performed with four different variant calling tool sets, for each sample sequenced in this study.
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