LOC_000SAPS.1

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India/LOC_000SAPS.1/2016

P. D. Yadav

National Institute of Virology, Maximum Containment Laboratory

Sample details

Collection date

2016

Earliest release date

2020-03-22

Sampling location

India (Vadodara District, Gujarat State)

Isolate name

NIV1614467

Data use terms

OPEN

Data use terms URL

https://#TODO-MVP/open

INSDC

NCBI release date

2020-03-22

INSDC accession L

MH396664.1

INSDC accession M

MH396665.1

INSDC accession S

MH396666.1

Host

human (Homo sapiens)

Submission details

Submission ID

MH396664.1.L/MH396665.1.M/MH396666.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2026-07-13 16:59:07 UTC

Date released

2026-07-13 17:02:26 UTC

Lineage

Segment S Lineage

IV.1

Files

Annotations

LOC_000SAPS.1.embl

Alignment and QC

Total SNPs M

1566

Total inserted nucs M

Total deleted nucs M

Length M

5402 (99.8%)

Total SNPs L

1642

Total inserted nucs L

Length L

12141 (99.9%)

Total SNPs S

226

Total inserted nucs S

165

Length S

1823 (99.2%)

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

L

G23T
A35G
G43T
T49C
C63G
C64T
T65C
T66C
T68C
G69A
G71C
C85T
G88A
G93A
A109G
C117A
A124G
T131A

M

T3G
A5T
A6C
G8T
A9C
A10C
A11G
A13T
T16G
G50C
A51G
A52T
G56T
T58A
T59A
T65A
C66T
T67C

S

A50G
G54A
G67A
C82T
G99A
G100A
A118G
C142T
C154A
T163C
C166T
G169A
T172C
C178A
T182C
G190A
T199C
C208T

Deletions

M

18, 297-305, 628-630, 678-689, 5172-5186

Insertions

L

ins_58:T, ins_11917:CA, ins_12053:CTAC, ins_12086:CTACTATCCCAC, ins_12108:TTTATTATTTCTGGGGTGTGGGGGGAAC

M

ins_0:CACACCGATCACATCACTCTTTCCCTACACC, ins_236:CCGTCAACAGACACTGCC, ins_365:GTTGCCATTGTCCAAACACAAGAAACAGAAGCACCC, ins_5202:CA, ins_5248:C

S

ins_1672:ACTCGGCCTCAGTTAGGACGCCCTCCCCACTGTTACCAACATGAAGCTGCTCGCAGCAACTGTGCTACTCATCACCATCTGCAGCCTTGAAGGAGCTTTGGTTCGGAGACAGTCAAAGGAGCCATGTGTGGAGAGCCTGGTTTCTCAGTACTTCCAGACCGTTAC

Amino acid substitutions

Substitutions called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references