L1 G5696A, C5756G, A5816T, T5855C, T5909C, A6023T, 6028delA, 6049insA, 6092delA, 6105delA, T6245C, A6314G, C6539A, *C6557T, A6559T, 6560delT, 6561delA, 6606insT, 6626insT, 6638delT, *A6665C, 6669delT, G6719A, A6779T, C6824T, *C6852T, 6857delA, C6863T, 6871delG, 6909delA, 6918delC, 6934delC, T6966C, C6968T, C6969T, T6972C, G6978A, A6983C, 6988delT, 6989delA, 6990delA, *G6992A, A6994G, T6999G, G7008A, 7011delC, C7017A, 7027delT, 7049delA, G7058A, G7062C, A7073T, 7075delT, 7076delT, 7077delA, 7098delA, C7106A, T7130G, 7135delG, G7144C *C5562G (Q2E), A5620G (Y21C), T5629C (F24S), T5638A (M27K), A5797C (K80T), G5829A (V91l), *C5862T (H102Y), *C6163A (T202N), G6171A (A205T), A6178C (N207T), C6240G (H228D), A6432G (T292A), A6445C (N296T), C6564A (P336T), G6652C (S365T), *A6693C (T379P), A6801T (T415S), 6901insAC (448insS), 6950delGT (465delD), G7033C (R492P), *G7058T (L500F), G7090A (R511Q), A7132C (K525T) 37 L1 T5675C, *G5698A, A5755C, *T6247C, A6316G, T6319C C6370T, A6391G, A6425C, C6541A, *A6565G, *C6559T, *A6667C, *G6721A, C6826T, *C6854T, *C6865T, T6889G, A6952G, *C6970T, *G6994A, T7027G, G7032A, A7072T, T7078C, A7141C *C5864T (H76Y), *C6165A (T176N), G6173A (A179T), *A6180C (N181T), C6182G (P182A), *A6434G (T266A), T6438G (V267G), A6445C (N296T), G6458A (D274N), G6582A (R315Q), T6689G (S351A), *A6695C (T353P), *A6803T(T389S), T7028G (L464V), A7148C (K504Q) 24 L2 A4242G, A4266C, *T4281C, A4299C, *A4410G, *G4428T, T4446G, *T4452C, *G4461A, A4467C, A4468C, C4525T, T4545G, *A4599C, A4626T, A4632C, *T4644A, T4647G, T4695C, *C4725T, A4788C, A4887G, G4938A, A4944G, *A4950G, *A5034T, A5073T, G5142A, T5286A, *G5379A, A5409G, T5412G, T5475A, T5478C, *C5487T, A5517G, T5523C, A5532G, A5622G C4253T (S6F), *T4600C (S122P), G4621A (D129N), G4654A (D140N), A4693C (T153P), A4811C (N192T), A4820G (E195S), *A4969G (T245A), G5008A (E258K), A5027C (N264T), T5041C (S269P), C5042A (S269Y), A5048C (N271H), T5060A (I275N), A5063C (N276T), A5152C (I306L), A5250C (E338D), A5256T (E340D), A5356C (I374L), T5357G (I374S), C5369T (S378V), *T5386G (S384A), *G5389A (V385I), A5466C (L410F), A5492C (I418T), *T5495C (I420T), A5505C (Q423H), *G5506A (A424T), A5518C (I428L), *T5368G (S378V), *C5564G (A443G), G5609A (R458Q) 24 L2 UTR/NCR2 A4150C, *C4151A, *A4157G, *T4158A, *C4164T, A4184T, T4186A, T4222C, T4231G, A4233C, A4234C 24 E1 *T921C, T1221C, T1446C, G1941A, T2301C, T2343C, *C2344T, T2470C, T2478C, T2778C C874T (P4S), *G1293T (Q143H), *T1297A (L145I), *G1363A (G167S), *T1421C (I186T), *A1842G (I326M), G2337A (M491I), *G2650A (E596K) 24 E2 *C3007T, *G3058A, A3187C, *A3253G, A3538C, T3694A C2988T (T78M), A3025C (E90D), C3161T (H136Y), *C3236G (H161D), *A3605G (Q286D), T3517A/C (T254K/N), T3566G (F271V), C3684A (T310K), A3181C (E142D), G3182A (A143T), T3224A (L157I), G3249A (R165Q), C3516A (T254K) 23 E2 T2914C, C3007T, G3058A, T3172G, *A3181C, A3187C, A3253G, T3259C, T3313G, T3664C, *C3684A, *T3694A, *T3706C, *C3787A, C3800G, *T3805G, T3820C, *T3847C C2988T (T78M), C3161T (H136Y), *C3159A(T135K), T3172G (I139M), *G3182A (A143T), A3208C (Q151H), *T3224A (L157I), C3236G (H161D), *G3249A (R165Q), A3285C (K177T), G3778T/C (W341C/W341C) 24 E2/E4 A3362G, *A3366C, T3371C, C3377G, T3387C, *C3410T, G3413A, A3605G *A3362G (N203D/A7A), A3366C (E204A/K9Q), T3371C (S206P), *C3377G (P208A/L12L), T3387C (I211T), *C3410T (P219S), G3413A (A220T), *C3516A (T254N/L59T), *T3517C (T254N/L59T), *A3538C (S261S/Q66P), *T3566G (F271V/H75Q), C3576T (S274L/ H79Y), G3585C (G277A/D82H), A3605G (N284D) 24 E6 *T286A, *A289G, *A532G *G145T (Q14D), *C335T (H78Y), *T350G (L83V), G176A (D25N), G188C (E29Q) 24 E6 A181C, T286A, A289G, G522DEL, A532G, C537DEL G145T (Q14H), G176A (D25N), G188C (E29Q), T311A (Y70N),*C335T (H78Y), A336G (H78C),*T350G (L83V), C506G (R135G) 37 E7 G666A, T687C, *T789C, *T795G *T732C (F57V), C790T (R76C) 24 E7 G666A, T687C, T730G, *T789C, *T795G *T732C (F57V), G823A (G88R), T844DEL (Frameshift), G849C (Q98H), A852DEL (Frameshift, K97N, P98H) 37 LCR *T7450C, C7394T, C7395T, A7482G, A7485C, G7489A, Int-del T 7497, C7689A, T7743G, A7729C, C7764T, C7786T, G7868A, G7521A, A7550G, T7568G, C7669T, G7703T, T7713G, T7714G, T7775A, G7826A 23 LCR

A7168G, T7176G, T7187C, *G7193T, A7227C, A7233C, A7376T, C7394T, C7395T, T7401C, G7427A, G7435A, *T7450C, A7482G, A7483C, *A7485C, *G7489A, *G7521A, A7550G, C7577T, C7655A, *C7669T, *C7689A, T7713G

*A7729C, *T7743G, *C7764T, A7773C, T7775A, *C7786T, C7792T, G7826A, T7827A, G7834T, G7868A, C7886G, C13T, C24T, A93T, A98C

24 West India L1 T5673C, G5696A, T5855C, T5909C, 6020delC, A6023T, 6105delA, T6245C, A6314G, C6265T, A6389G, C6539A, 6554delA, *C6557T, *A6665C, 6706delA, G6719A, *C6852T, T6860C, C6863T, A6935T, A6947G, C6968T, A6983C, *G6992A, T7025G, G7058A, T7076C, A7154G *C5562G (Q2E), C5600A (Y14X), C5609A (D17E), *C5862T (H102Y), A6021G (T155A), G6024A (E156K), *C6163A (T202N), G6171A (A205T), A6178C (N207T), C6240G (H228D), G6261T (D235Y), C6388T (R277L), A6432G (T292A), G6495T (A313S), 6563delA (K335X), *A6693C (T379P), A6801T (T415S), G6879A (E441K), 6901insAC (448insS), G6945A (E463K), 6950delGT (465delD), G7008C (D484H), *G7058T (L500F), A7087C (K510T), G7090A (R511Q), T7150A (L531Q), A7154C (X532Y) 37 E6 A187G *T350G (L83V), *350T, T310G (F69L), A512T (M137L) 25 E6 A111G, T286A, A289G, A320DEL, INS342G, G522T, A529G, T530A, A532DEL, A532C, A532G, A562DEL A131G (R10G), G145T (Q14H), C158A (L19M), G176A (D25N), A182T (I27L), C315G (S71C), *C335T (H78Y), *T350G (L83V), C479T (H126Y), T521C (C140R), T521G (C140V), INS524A (R141K), C531T (S143I) 37 E7 *T789C, *T795G A619T (T20S), *T732C (F57V), A746DEL (Frame shift), G829DEL (V90C, C91A), T844DEL (Frame shift) 37 North India L1 A6667C,A6691G, A6721G, C6854T, T6889G, C6970T, G6994A, C6865T *A6695C (T353P), A6803T(T389S), A6964C, C6906T (S423F), A6924C (Q429P) 27 L1 T5673C, T5681C, G5696A, A5795G, A5813G, A5816T, A5834G, T5909C, C5967T, A6023T, A6068G, A6182C, T6245C, G6278A, C6365T, A6389G, A6452G, A6518G, C6539A, *C6557T, *A6665C, G6719A, A6779T, *C6852T, C6863T, T6887G, G6936A, C6968T, *G6992A, T7076C, A7094G *C5562G (Q2E), A5620G (Y21C), *C5862T (H102Y), G5871T (D105Y), *C6163A (T202N), A6178C (N207T), C6240G (H228D), C6388T (R277L), A6432G (T292A), G6495T (A313S), T6573A (L338l), T6634A (V359D), *A6693C (T379P), A6801T (T415S), G6879A (E441K), 6901insAC (448insS), 6950delGT` (465delD), G7008C (D484H), *G7058T (L500F), G7090A (R511Q) 37 E6 T286A, A289G, A532G G145T (Q14D), C335T (H78Y), *T350G (L83V), T527A (S142T) 27 E6 T286A, A289G. A532G T109C, A131G (R10G), G145T (Q14D), A169C (T-P), G176A (D25N), T178G (D25E), G293A (D-N), C335T (H78Y), T350G (L83V), 403, G507A (R-E), G525T (R-I) 28 E6 T286A, A289G G145T (Q14H), *C158T, C335T (H78Y), *T350G (L83V) 30 E6 A169C, G267A, T286A, A289G, G293A, G507A, G525T, A532G A131G (R10G), *G145T (Q14H), G176A (D25N), T178G (D25E), C315G (S71C), *C335T (H78Y), *T350G (L83V) 37 E7 G666A, T789C, T795G, T828C T732C (F57V) 27 E7 G663A, G826T, A746T, T789C, T795G A647G (N29S), T732C (F57V) 28 E7 G663A, A746T, *T789C, *T795G, T843C A647G (N29S), *T732C (F57V), G823A (G88R), A826T (I89F), T846C (S95L) 37 LCR *G7521A, A7636C, C7689A, *T7714G, C7792T, G7826A, A7839C, T7743G, *C7764T, C13T, C7669T, C7678T, A7729C, C7786T, G7799A, G7834T, C7886G 27 South India L1 DELETION AND INSERTION AT 6695, 6722,6733, 6736, 6737, 6738 and 6744 SNPs at 6722, 6742, 6743, 6759, *6760, *6726, *6729, *6730, *6732, *6738, *6739, *6741, *6744, *6759. 33 L1 55595insC, T5597A, G5636A, G5696A, T5801G, A5847C, T5906C, T5909C, T5999G, A6023T, 6028delA, A6068G, A6177C, A6200G, T6245C, 6253delG, 6283insA, G6302A, A6314G, C6539A, T6553C, *C6557T, A6561T, 6564delC, A6581C, A6581T, T6608C, 6658delA, *A6665C, G6719A, G6737T, *C6852T, C6863T, T6911A, T6914C, A6947G, C6968T, *G6992A, A7028G, G7058A, T7076C *C5562G (Q2E), A5568C (T4P), C5600A (Y14X), A5602G (E15G), A5730C (N58H), *C5862T (H102Y), *C6163A (T202N), A6166T (N2031), G6171A (A205T), A6178C (N207T), C6240G (H228D), A6293C (E245D), C6352T (S265L), A6432G (T292A), A6445C (N296T), A6490C (N311T), C6502T (S315L), A6504C (N316H), T6560A (N334K), 6563delA (K335X), C6564A (P336T), C6565T (P336L), *A6693C (T379P), A6801T (T415S), 6901insAC (448insS), 6950delGT (465delD), A6961C (K468T), C6970A (T471N), A6997G (K480R), *G7058T (L500F), G7084A (G509E), 7093C (K512T) 37 L1 5605delA, 5640delT, G5696A, A5834G, T5909C, T6230C, T6245C, A6314G, A6452G, *C6557T, A6561T, 6654delA, 6663insA, *A6665C, G6719A, *C6852T, C6863T, A6891C, C6968T, T6971G, A6979G, *G6992A, G7058A, 7120insTC *C5562G (Q2E), T5597G (C13W), T5598G (Y14D), G5607A (D17N), *C5862T (H102Y), *C6163A (T202N), G6171A (A205T), A6178C (N207T), C6240G (H228D), A6432G (T292A), A6458G (D300E), T6560A (N334K), 6563delA (K335X), *A6693C (T379P), A6801T (T415S), 6901insAC (448insS), 6950delGT (465delD), G7008C (D484H), C7011A (L4851), *G7058T (L500F), T7110A (S518T) 37 L1 T5673C, A5687G, G5696A, A5702C, A5834G, T5909C, 6022delC, A6023T/C, G6059A, A6068G, 6087delT, T6245C, T6269C, A6314G, T6317A, A6389G, A6452G, T6482C, C6539A, A6554C, *C6557T, A6581T, A6656G, *A6665C, A6668G, G6719A, C6726T, G6836A, *C6852T, T6860C, C6863T, G6893A, A6938C, A6947G, C6968T, A6989G, *G6992A, G7058A, T7076C, T7130A, C7143A, T7145G C5562G (Q2E), A5620G (Y21C), C5862T (H102Y), *C6163A (T202N), A6178C (N207T), C6240G (H228D), A6432G (T292A), 6563delA (K335X), *A6693C (T379P), A6801T (T415S), T6822C (S422P), 6901insAC (448insS), A6947C (E463D), 6950delGT (465delD), C6957T (L467F), *G7058T (L500F), C7117A (T520N), A7147C (K530T) 37 E2 A2983G, A3538C, T3664A, C3684A, T3694A, T3706C, G3778T C3161T (H136Y), C3516A (T254N), T3517C (T254N), T3566G (F271V), T3371C(S206P), C3159A (T135K), A3362G (N203D), C3410T (P219S), G3449A, G3778A 32 E6 350T, *T350G (L83V), *C335T (H78Y), *G145T (Q14D), T419G (C106G) 31 E6 T286A, A289G, A508C, A532G, A536DEL G145T (Q14H), T178G (D25E), T329C (Y76H), *C335T (H78Y), G491A (G130S), C528T (S142L) 37 E6 T254DEL, T265DEL, T279DEL, T286A, A289G, A532G G145T (Q14H), T178G (D25E), T179G (I26V), G188A (E29K), *C335T (H78Y), *T350G (L83V), A442C (E113D), A526T (R141S), T527A (S142T) 37 E6 T286A, A289G, A532G G145T (Q14H), T183G (I27R), G205T (K34N), C245T (R48W), T308C (F69L), *C335T (H78Y), *T350G (L83V), T402C (L100S), G491A (G130S) 37 E7 T732C, T795G *A647G (N29S), *C790T (R76C) 31 E7 *T789C, *T795G, T843C A647G (N29S), *T732C (F57V), C747DEL (Frame shift), G842DEL (Frame shift), T844DEL (Frame shift), T846C (S95L) 37 E7 INS668GGA, *T789C, *T795G, T843C A645C (L28F), A647G (N29S), *T732C (F57V), T846C (S95L) 37 E7 G585A, T756C, *T789C, *T795G, C854DEL A619T (T20S), G709A (A50T), C712T (H51Y), *T732C (F57V), C747DEL (Frame shift), A826DEL (Frame shift), A826T (I89F), T844DEL (Frame shift), A852DEL (Frame shift, K97N, P98H) 37 Central India E6 A229G GAT114TAC (D4Y), A225G (E41G), C240G (A46G), T244G (F47V), *C315G (S71C), A334T (R77S), *T350G (L83V), T400G (L99V), C422A (Q107K), C523A (C140Stop), G545A (E148K) 34 E7 C834T, C836A T573G (D4E), *G823C (G88R), *T838C (I93T), *T841A (C94S) 34 East, Central and North India L1 T5675C, *G5698A, A5752C, A5755C, C5864T, *T6247C, A6316G, T6319C, C6370T, A6391G, A6425C, C6541A, C6559T, A6565G, T6661C, A6667C, G6721A, C6826T, *C6854T, C6865T, T6889G, A6952G, C6970T, G6994A, T7027G, G7031T, G7032A, G7060A, A7072T, T7078C, T7123C, A7141C G6069C (R144T), *C6165A (T176N), G6173A (A179T), A6180C (N181T), C6182G (P182A), *A6434G (T266A), T6438G (V267G), A6445C (E269D), G6458A (D274N), A6492T (N285I), G6582A (R315Q), T6689G (S351A), *A6695C (T353P), A6803T (T389S), T7028G (L464V), *G7060T (L474F), A7148C (K504Q) 36 L2 A4242G, A4266C, T4281C, A4299C, A4410G, A4413C, G4428T, T4446G, T4452C, G4461A, A4467C, A4468C, A4504C, C4525T, T4527C, T4545G, G4563A/T, T4572G, A4599C, A4626T, A4632C, T4644A, T4647G, T4695C, *C4725T, A4788C, C4848T, A4887G, G4938A, A4944G, A4950G, A5034T, A5073T, G5142A, A5187C, T5286A, G5379A, T5403C/G, A5409G, T5412G, T5475A, T5478C, C5487T, A5517G, T5523C, A5532G, A5622G C4253T (S6F), A4368C (Q44H), T4600C (S122P), G4621A (D129N), G4654A (D140N), A4693C (T153P), A4811C (N192T), A4820G (E195S), A4821C (I196L), C4825T & C4826A (P197Y), A4969G (T245A), G5008A (E258K), A5027C (N264T), T5041C (S269P), C5042A (S269Y), A5048C (N271H), A5059G (I275V), T5060A (I275N), A5063C (N276T), A5152C (I306L), *A5226T/C (L330F/F), C5231G (T332S), G5236C/A (D334H/N), A5250C (E338D), A5256T (E340D), A5356C (I374L), T5357G (I374S), T5368G & C5369T (S378V), T5386G (S384A), G5389A (V385I), A5466C (L410F), A5492C (I418T), T5495C (I420T), A5505C (Q423H), G5506A (A424T), C5509T (P425S), A5518C (I428L), C5564G (A443G), G5609A (R458Q) 36 L2 UTR/NCR2 A4150C, C4151A, *T4152G/A, A4157G, T4158A, *C4164T, A4184T, T4186A, T4222C, *T4228C/G/A, T4231G, A4233C, A4234C 36 E1 T921C, T1221C, T1446C, G1941A, T2301C, T2343C, C2344T, T2470C, T2478C, T2778C C874T (P4S), G1293T (Q143H), T1297A (L145I), G1363A (G167S), T1421C (I186T), A1842G (I326M), T1920G/C (D352E/D), G2337A (M491I), G2650A (E596K) 39 E2

T2914C, C3007T, G3058A, A3187C, A3253G, T3259C, T3313G, C3436A, A3538C, T3640C, T3664C, *C3684A, T3694A, T3706C, G3778T/C, C3787A, C3800G, T3805G, T3820C, T3847C

A2919C (N55T), C2988T (T78M), C3159A (T135K), C3161T (H136Y), T3172G (I139M), A3181C (E142D), G3182A (A143T), A3208C (Q151H), *T3224A (L157I), C3236G (H161D), G3249A (R165Q), A3285C (K177T), C3348T (S198F), A3362G (N203D), A3366C (E204A), T3371C (S206P), C3372A (S206Y), C3377G (P208A), T3387C (I211T), *C3410T (P219S), G3413A (A220T), C3516A (T254N), T3517C (T254N), T3566G (F271V), C3576T (S274L), G3585C (G277A), A3605G (N284D) 36 E4 A3362G, T3371C, C3377G, T3387C, *C3410T, G3413A, A3605G A3366C (K9Q), C3372A (P11T), C3436A (S32stop), C3516A (L59T), T3517C (L59T), A3538C (Q66P), T3566G (H75Q), C3576T (H79Y), G3585C (D82H) 36 LCR A7168G, T7176G, T7187C, G7193T, A7197C, A7227C, *A7233C, A7266G/C, A7376T, C7394T, C7395T, T7401C, G7427A, G7435A, *T7450C, A7482G, A7483C, *A7485C, *G7489A, *G7521A, A7550G, C7577T, C7655A, *C7669T, *C7689A, T7713G, T7714G/A, A7729C, T7743G, C7764T, C7792T, A7773C, T7775A, C7786T, G7826A, T7827A, G7834T, G7868A, C7886G, C13T, C24T, A93T, A98C 36 West and South India L1

*C5990T,

*C5695T

A4941C (N56T), C5000T (H76Y), A5049C (N92T), A5248C (L158F), T5307G (V178G), A5316C/T (N181T/I), A5481C (K236T), A6101C (K443Q), A6135C (K454T), A6198G (K475R), C5301A (T176N), G5309A (A179T), *A5570G (T266A), A5628C (N285T), T5662A (S296R), *A5831C (T353P), A5939T (T389S), T5960C (S396P) and *G6196A/T (L474F) 40 L2 (L75F), (T85A), (T94A), (S122P/A), (S134R), (T245A), (L266F), *(S269P), (S270N), (D272N), (N273S), (I306L), *(L330F), (T332S), *(D334N), (D334H), (D334T), (E338D), (Q342L), (T352P), (H354Q), (T377S), (S378V/F), (S384A), (V385I), (L390F), (I418M), (I420T), (Q423H), (A424T), (S426A), (I428L), (A443G) 42 LCR *G6657A, *T6586C, *A6865C, A6475T, T6554C, G6606T, C6701T, A6737T, A6771T, C6805G, T6836G, T6847G, A6866C, T6917C, T6926A, T6967A, A6973C, A6975G, G6978A, G6988A, G6992A, G7004C, G7005A, C7012A, T7015C, C7025T, C7055T, C7066T, C6530T, C6531T, A6618G, A6621C, G6625A, T6704G, A6772C, C6805T/G, C6825A, T6849G, T6850G, T6879G, C6900T, C6922T, C6928T, G6962A, G6970T, G7004A, C7022G 41 South and East India E6 A532G, T286A, A289G, T421G, G522C *T350G (L83V), C335T (H78Y), A276C (N58S) 35