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PP_000RDZ5.1

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Pakistan/PP_000RDZ5.1/2023-09-25

M. Umair, S. A. Haider, Z. Jamal, M. Ammar, R. Hakim, Q. Ali & M. Salman

National Institute of Health, Department of Virology

Sample details

Collection date

2023-09-25

Sampling location

Pakistan (Asia)

Isolate name

CCHF/NIHPAK-9/2023

Data use terms

OPEN

Data use terms URL

https://pathoplexus.org/about/terms-of-use/open-data

Lineage

Segment S Lineage

IV.1

INSDC

INSDC accession L

OR964929.1

INSDC accession M

OR964940.1

INSDC accession S

OR964918.1

NCBI release date

2023-12-26

Host

human (Homo sapiens)

Submission details

Submission ID

OR964929.1.L/OR964940.1.M/OR964918.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2024-08-27 12:10:45 UTC

Date released

2024-08-27 12:16:35 UTC

Earliest release date

2023-12-26

Alignment and QC

Length L

12122 (99.8%)

# of SNPs L

1639

# of inserted bases L

# of unknown bases L

Length S

1630 (96.9%)

# of SNPs S

225

# of inserted bases S

# of unknown bases S

Length M

5324 (98.3%)

# of SNPs M

1026

# of inserted bases M

# of deleted bases M

# of unknown bases M

# of frame shifts M

Frame shifts M

GPC:724-1685(nt:2262-5147)

Nucleotide mutations

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

Substitutions

L

G23T
A35G
G43T
C48T
T49C
C63G
C64T
T65C
T66C
T68C
G69A
G71C
G88A
G93A
A109G
C117A
A124G
T131A

M

G50T
A51G
G56A
A57C
A70G
T71A
T72C
G76T
A80G
T83C
C85T
T86C
A90G
T91C
C92T
A93G
T98C
T100C

S

A50G
G54A
G76A
T79C
A85G
T88C
G91A
T106C
A109G
A118G
A121G
C142A
T144A
C145T
A148G
C166T
G169A
G171A

Deletions

M

5257

Insertions

L

ins_58:T, ins_11915:AA, ins_12054:TAAAATTTT, ins_12083:ACTATTC, ins_12108:TTTGTTATTTC

M

ins_2261:A, ins_2915:A, ins_5170:G

S

ins_1574:T

Amino acid substitutions

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