GS_00BUMYG.1

Display Name: USA/GS_00BUMYG.1/2025-01-02
Paull, J.; Messer, K.; Adams, G.; Nabatanzi, D.; Dobbins, S.; Tomkins-Tinch, C.; Mboowa, G.; Luebbert, L.; Worby, C.; Wewior, N.; Samani, P.; DeRuff, K.; Blumenstiel, B.; Moreno, G.; Earl, A.; Gnirke, A.; MacInnis, B.; Sabeti, P.; Lemieux, J.; Park, D.

Submission details

Submission ID
PV242509.1.seg1/PV242510.1.seg2/PV242511.1.seg3/PV242512.1.seg4/PV242513.1.seg5/PV242514.1.seg6/PV242515.1.seg7/PV242516.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-11 10:32:49 UTC
Date released
2025-03-11 11:08:10 UTC

Authors

Author affiliations
Broad Institute of MIT and Harvard, Infectious Disease and Microbiome Program

INSDC

Bioproject accession
PRJNA1052714
Biosample accession
SAMN47202825
INSDC accession seg1
PV242509.1
INSDC accession seg2
PV242510.1
INSDC accession seg3
PV242511.1
INSDC accession seg4
PV242512.1
INSDC accession seg5
PV242513.1
INSDC accession seg6
PV242514.1
INSDC accession seg7
PV242515.1
INSDC accession seg8
PV242516.1
NCBI release date
2025-03-07
SRA run accession
SRR32579596

Clade

Clade ha
V1A.3a.2
Clade na
B.7

Alignment states and QC metrics seg3

Completeness seg3
97.19%
Length seg3
2182
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
45
Total unknown nucs seg3
0

Alignment states and QC metrics seg4

Completeness seg4
98.83%
Length seg4
1854
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
57
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
99.20%
Length seg5
1784
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
48
Total SNPs seg5
32
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
100.00%
Length seg6
1543
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
142
Total SNPs seg6
35
Total unknown nucs seg6
0

Alignment states and QC metrics seg7

Completeness seg7
98.87%
Length seg7
1156
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
22
Total SNPs seg7
18
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
98.22%
Length seg8
1054
Total ambiguous nucs seg8
0
Total deleted nucs seg8
5
Total frame shifts seg8
0
Total inserted nucs seg8
12
Total SNPs seg8
19
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
Massachusetts
Collection date
2025-01-02
Isolate name
MA-Broad_MGH-23022

Host

Host name scientific
Homo sapiens
Host taxon id
9606

Alignment states and QC metrics seg1

Length seg1
2361

Alignment states and QC metrics seg2

Length seg2
2278

INSDC seg4

Lineage seg4
vic

Nucleotide mutations

Mutations called relative to the CY115157.1, CY115158.1, CY115156.1, KX058884.1, CY115154.1, CY073894.1, CY115152.1 & CY115155.1 references

Substitutions

seg3

  • seg3:T111C
  • seg3:C117T
  • seg3:T339C
  • seg3:G414A
  • seg3:T423C
  • seg3:G549A
  • seg3:T587C
  • seg3:T588C
  • seg3:A618G
  • seg3:T654C
  • seg3:A771G
  • seg3:C813T
  • seg3:G867A
  • seg3:C897T
  • seg3:A935G
  • seg3:G936A
  • seg3:C1006T
  • seg3:A1054G

    • seg4

  • seg4:A84G
  • seg4:C252A
  • seg4:G267A
  • seg4:C270T
  • seg4:A285G
  • seg4:G297A
  • seg4:G312T
  • seg4:A318G
  • seg4:A351G
  • seg4:C375T
  • seg4:C378T
  • seg4:A427G
  • seg4:C441T
  • seg4:T444C
  • seg4:G457A
  • seg4:G460A
  • seg4:A463G
  • seg4:A477G

    • seg5

  • seg5:T46C
  • seg5:C178T
  • seg5:A224G
  • seg5:A235G
  • seg5:T298C
  • seg5:C313T
  • seg5:G361A
  • seg5:A373G
  • seg5:C380T
  • seg5:G412A
  • seg5:A454G
  • seg5:C523T
  • seg5:C608T
  • seg5:A634G
  • seg5:C703T
  • seg5:A763G
  • seg5:C841T
  • seg5:A883G

    • seg6

  • seg6:T9C
  • seg6:C125A
  • seg6:T155C
  • seg6:G189A
  • seg6:T212C
  • seg6:G279A
  • seg6:A358G
  • seg6:C394T
  • seg6:C399T
  • seg6:C429T
  • seg6:G462A
  • seg6:A504G
  • seg6:C519T
  • seg6:A660C
  • seg6:T714A
  • seg6:T735C
  • seg6:C849T
  • seg6:T879C

    • seg7

  • seg7:C33T
  • seg7:C46T
  • seg7:A83G
  • seg7:T125A
  • seg7:A143G
  • seg7:G316A
  • seg7:A419G
  • seg7:A452G
  • seg7:G482A
  • seg7:G498A
  • seg7:G500T
  • seg7:G521A
  • seg7:G536A
  • seg7:A566G
  • seg7:C656T
  • seg7:C802T
  • seg7:A919G
  • seg7:A967G

    • seg8

  • seg8:G6A
  • seg8:A118G
  • seg8:T163C
  • seg8:G190A
  • seg8:T341C
  • seg8:A352C
  • seg8:T391C
  • seg8:C419T
  • seg8:G478A
  • seg8:C604T
  • seg8:A610T
  • seg8:C632T
  • seg8:G661A
  • seg8:C666T
  • seg8:T775C
  • seg8:G818A
  • seg8:C882T
  • seg8:A950G
  • seg8:T963C
    • Deletions
    seg4:562-570, seg8:25, seg8:26, seg8:38-40
    Insertions
    ins_seg8:0:GCAGAAGCAGAG, ins_seg7:0:AGCAGAAGCACGCACTTTCTTA, ins_seg6:0:AGCAGAAGCAGAGCATCTTCTCAAAACTGAAGCAAATAGCCCAAAAATGAACA, ins_seg6:1401:TGGGGGAGTGGTTAGGTCTGTTCTAAACCCTTTGTTCCTATTTTATTTGAACAATTGTCCTTACTAAACTTAATTGTTTCTGAAAAATG, ins_seg5:1750:CGTTTGGAACATGGGTGTTTATTCTCATTAAAATAAATATAAAAAATG

    Amino acid mutations

    Mutations called relative to the CY115157.1, CY115158.1, CY115156.1, KX058884.1, CY115154.1, CY073894.1, CY115152.1 & CY115155.1 references

    Substitutions

    HA1

  • HA1:I117V
  • HA1:A127T
  • HA1:E128K
  • HA1:N129D
  • HA1:K136E
  • HA1:P144L
  • HA1:N150K
  • HA1:E183K
  • HA1:G184E
  • HA1:N197E
  • HA1:A199T
  • HA1:A202V
  • HA1:K203R
  • HA1:G256E
  • HA1:R279K

    • HA2

  • HA2:D71N
  • HA2:R151K

    • M1

  • M1:T15I
  • M1:R105K
  • M1:A166T

    • NA

  • NA:P42Q
  • NA:L52S
  • NA:V71A
  • NA:I120V
  • NA:K220N
  • NA:S295R
  • NA:N340D
  • NA:K343E
  • NA:E358K
  • NA:G378E
  • NA:D384G
  • NA:A395V
  • NA:V401I

    • NEP

  • NEP:L30S
  • NEP:S93P

    • NP

  • NP:T66A
  • NP:V453A

    • NS1

  • NS1:Y104H
  • NS1:K107N
  • NS1:L130F
  • NS1:H201Y
  • NS1:A212V
  • NS1:V263M

    • PA

  • PA:V196A
  • PA:K312R
  • PA:T352A
  • PA:S530T
  • PA:F709V
  • PA:N714S
  • PA:I723V
    • Deletions
    HA1:162-164, NEP:3, NS1:3
    Insertions
    None