Frame shift ORF7a:empty range is confusing

[corneliusroemer]

I remember we talked about this on Slack, we seem to sometimes output ORF7a:empty range into the tsv - which is not ideal since it breaks assumptions.

Maybe we can at least document what it means, and maybe fix it. I think this occurs if there's a frame shift in the stop codon?

Here are a few sample Genbank URLs:

OV623283.1
OV731935.1
OW351812.1
OU254502.1

empty_range.fasta.txt

[ivan-aksamentov]

Potentially related Slack threads:

• https://neherlab.slack.com/archives/C015PFP5V44/p1655384957174379
• https://neherlab.slack.com/archives/C015PFP5V44/p1637167275054600

Results of Nextclade run are attached

nextclade.json.txt
nextclade.tsv.txt

[ivan-aksamentov]

Click to show the result

jq '.results[0].frameShifts' nextclade.json | prettyjson

- 
  geneName:     ORF7a
  nucRel: 
    begin: 365
    end:   366
  nucAbs: 
    begin: 27758
    end:   27759
  codon: 
    begin: 122
    end:   122
  gapsLeading: 
    codon: 
      begin: 101
      end:   122
  gapsTrailing: 
    codon: 
      begin: 122
      end:   122
  codonMask: 
    begin: 101
    end:   122

Click to show the result

jq '[ .results[0].aaDeletions[] | select( .gene == "ORF7a" ) ]' nextclade.json | prettyjson

- 
  gene:             ORF7a
  refAA:            F
  codon:            100
  codonNucRange: 
    begin: 27693
    end:   27696
  refContext:       ATTTTTCTT
  queryContext:     ATTT-----
  contextNucRange: 
    begin: 27690
    end:   27699
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            L
  codon:            101
  codonNucRange: 
    begin: 27696
    end:   27699
  refContext:       TTTCTTATT
  queryContext:     T--------
  contextNucRange: 
    begin: 27693
    end:   27702
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            I
  codon:            102
  codonNucRange: 
    begin: 27699
    end:   27702
  refContext:       CTTATTGTT
  queryContext:     ---------
  contextNucRange: 
    begin: 27696
    end:   27705
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            V
  codon:            103
  codonNucRange: 
    begin: 27702
    end:   27705
  refContext:       ATTGTTGCG
  queryContext:     ---------
  contextNucRange: 
    begin: 27699
    end:   27708
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            A
  codon:            104
  codonNucRange: 
    begin: 27705
    end:   27708
  refContext:       GTTGCGGCA
  queryContext:     ---------
  contextNucRange: 
    begin: 27702
    end:   27711
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            A
  codon:            105
  codonNucRange: 
    begin: 27708
    end:   27711
  refContext:       GCGGCAATA
  queryContext:     ---------
  contextNucRange: 
    begin: 27705
    end:   27714
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            I
  codon:            106
  codonNucRange: 
    begin: 27711
    end:   27714
  refContext:       GCAATAGTG
  queryContext:     ---------
  contextNucRange: 
    begin: 27708
    end:   27717
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            V
  codon:            107
  codonNucRange: 
    begin: 27714
    end:   27717
  refContext:       ATAGTGTTT
  queryContext:     ---------
  contextNucRange: 
    begin: 27711
    end:   27720
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            F
  codon:            108
  codonNucRange: 
    begin: 27717
    end:   27720
  refContext:       GTGTTTATA
  queryContext:     ---------
  contextNucRange: 
    begin: 27714
    end:   27723
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            I
  codon:            109
  codonNucRange: 
    begin: 27720
    end:   27723
  refContext:       TTTATAACA
  queryContext:     ---------
  contextNucRange: 
    begin: 27717
    end:   27726
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            T
  codon:            110
  codonNucRange: 
    begin: 27723
    end:   27726
  refContext:       ATAACACTT
  queryContext:     ---------
  contextNucRange: 
    begin: 27720
    end:   27729
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            L
  codon:            111
  codonNucRange: 
    begin: 27726
    end:   27729
  refContext:       ACACTTTGC
  queryContext:     ---------
  contextNucRange: 
    begin: 27723
    end:   27732
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            C
  codon:            112
  codonNucRange: 
    begin: 27729
    end:   27732
  refContext:       CTTTGCTTC
  queryContext:     ---------
  contextNucRange: 
    begin: 27726
    end:   27735
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            F
  codon:            113
  codonNucRange: 
    begin: 27732
    end:   27735
  refContext:       TGCTTCACA
  queryContext:     ---------
  contextNucRange: 
    begin: 27729
    end:   27738
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            T
  codon:            114
  codonNucRange: 
    begin: 27735
    end:   27738
  refContext:       TTCACACTC
  queryContext:     ---------
  contextNucRange: 
    begin: 27732
    end:   27741
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            L
  codon:            115
  codonNucRange: 
    begin: 27738
    end:   27741
  refContext:       ACACTCAAA
  queryContext:     ---------
  contextNucRange: 
    begin: 27735
    end:   27744
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            K
  codon:            116
  codonNucRange: 
    begin: 27741
    end:   27744
  refContext:       CTCAAAAGA
  queryContext:     ---------
  contextNucRange: 
    begin: 27738
    end:   27747
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            R
  codon:            117
  codonNucRange: 
    begin: 27744
    end:   27747
  refContext:       AAAAGAAAG
  queryContext:     ---------
  contextNucRange: 
    begin: 27741
    end:   27750
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            K
  codon:            118
  codonNucRange: 
    begin: 27747
    end:   27750
  refContext:       AGAAAGACA
  queryContext:     ---------
  contextNucRange: 
    begin: 27744
    end:   27753
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            T
  codon:            119
  codonNucRange: 
    begin: 27750
    end:   27753
  refContext:       AAGACAGAA
  queryContext:     ---------
  contextNucRange: 
    begin: 27747
    end:   27756
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            E
  codon:            120
  codonNucRange: 
    begin: 27753
    end:   27756
  refContext:       ACAGAATGA
  queryContext:     --------A
  contextNucRange: 
    begin: 27750
    end:   27759
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64
- 
  gene:             ORF7a
  refAA:            *
  codon:            121
  codonNucRange: 
    begin: 27756
    end:   27759
  refContext:       GAATGATTG
  queryContext:     -----ATTG
  contextNucRange: 
    begin: 27753
    end:   27762
  nucSubstitutions: 
    (empty array)
  nucDeletions: 
    - 
      start:  27694
      length: 64

Click to show the result

jq '[ .results[0].qc.stopCodons ]' nextclade.json | prettyjson

- 
  score:                  0
  status:                 good
  stopCodons: 
    (empty array)
  totalStopCodons:        0
  stopCodonsIgnored: 
    (empty array)
  totalStopCodonsIgnored: 0

[ivan-aksamentov]

I'll leave the scientific analysis and documenting it to you, but let's see what can be improved in terms of the algorithm or user interface.