Data StandardΒΆ

The standardized column names used by the Change-O tab-delimited database format are shown in the table below. Most tools do not require every column. The columns required by, and added by, each individual tool are described in the commandline usage documentation. The ordering of the columns does not matter.

Column Name Type Description
MakeDb - Standard Annotations    
SEQUENCE_ID string Unique sequence identifier
SEQUENCE_INPUT string Input sample nucleotide sequence
SEQUENCE_VDJ string Ungapped sample V(D)J nucleotide sequence
SEQUENCE_IMGT string IMGT-gapped sample V(D)J nucleotide sequence
FUNCTIONAL logical T: sample V(D)J sequence is predicted to be functional
IN_FRAME logical T: sample junction region nucleotide sequence is in-frame
STOP logical T: stop codon is present in sample V(D)J nucleotide sequence
MUTATED_INVARIANT logical T: invariant amino acids properly encoded by sample V(D)J sequence
INDELS logical T: sample V(D)J nucleotide sequence may contain insertions and/or deletions
V_CALL string V allele assignment(s)
D_CALL string D allele assignment(s)
J_CALL string J allele assignment(s)
V_SEQ_START integer Position of first V nucleotide in SEQUENCE_INPUT
V_SEQ_LENGTH integer Number of V nucleotides in SEQUENCE_INPUT
V_GERM_START_IMGT integer Position of V_SEQ_START in IMGT numbered germline V(D)J sequence
V_GERM_LENGTH_IMGT integer Length of the IMGT numbered germline V alignment
NP1_LENGTH integer Number of of nucleotides between sample V and D sequences
D_SEQ_START integer Position of first D nucleotide in SEQUENCE_INPUT
D_SEQ_LENGTH integer Number of D nucleotides in SEQUENCE_INPUT
D_GERM_START integer Position of D_SEQ_START in germline V(D)J nucleotide sequence
D_GERM_LENGTH integer Length of the germline D alignment
NP2_LENGTH integer Number of nucleotides between sample D and J sequences
J_SEQ_START integer Position of first J nucleotide in SEQUENCE_INPUT
J_SEQ_LENGTH integer Number of J nucleotides in SEQUENCE_INPUT
J_GERM_START integer Position of J_SEQ_START in germline V(D)J nucleotide sequence
J_GERM_LENGTH integer Length of the germline J alignment
JUNCTION_LENGTH integer Number of junction nucleotides in SEQUENCE_VDJ
JUNCTION string Ungapped sample junction region nucletide sequence
MakeDb - Optional Region Annotations    
FWR1_IMGT string IMGT-gapped sample FWR1 nucleotide sequence
FWR2_IMGT string IMGT-gapped sample FWR2 nucleotide sequence
FWR3_IMGT string IMGT-gapped sample FWR3 nucleotide sequence
FWR4_IMGT string IMGT-gapped sample FWR4 nucleotide sequence
CDR1_IMGT string IMGT-gapped sample CDR1 nucleotide sequence
CDR2_IMGT string IMGT-gapped sample CDR2 nucleotide sequence
CDR3_IMGT string IMGT-gapped sample CDR3 nucleotide sequence
MakeDb - IMGT Optional Annotations    
N1_LENGTH integer N nucleotides 5’ of the D-segment
N2_LENGTH integer Nucleotides 3’ of the D-segment
P3V_LENGTH integer Palindromic nucleotides 3’ of the V-segment
P5D_LENGTH integer Palindromic nucleotides 5’ of the D-segment
P3D_LENGTH integer Palindromic nucleotides 3’ of the D-segment
P5J_LENGTH integer Palindromic nucleotides 5’ of the J-segment
D_FRAME integer D-REGION reading frame
V_SCORE float Alignment score for the V
V_IDENTITY float Alignment identity for the V
J_SCORE float Alignment score for the J
J_IDENTITY float Alignment identity for the J
MakeDb - IgBLAST Optional Annotations    
CDR3_IGBLAST_NT string CDR3 nucleotide sequence assigned by IgBLAST
CDR3_IGBLAST_AA string CDR3 amino acid sequence assigned by IgBLAST
V_SCORE float Alignment score for the V
V_IDENTITY float Alignment identity for the V
V_EVALUE float E-value for the alignment of the V
V_BTOP string BTOP for the alignment of the V
J_SCORE float Alignment score for the J
J_IDENTITY float Alignment identity for the J
J_EVALUE float E-value for the alignment of the J
J_BTOP string BTOP for the alignment of the J
MakeDb - iHHMune-Align Optional Annotations    
HMM_SCORE float Alignment score for the V(D)J
CreateGermlines Annotations    
GERMLINE_VDJ string Full Ungapped germline V(D)J nucleotide sequence
GERMLINE_VDJ_V_REGION string Ungapped germline V segment nucleotide sequence
GERMLINE_VDJ_D_MASK string Ungapped germline V(D)J nucleotides sequence with Ns masking the NP1-D-NP2 regions
GERMLINE_IMGT string Full IMGT-gapped germline V(D)J nucleotide sequence
GERMLINE_IMGT_V_REGION string IMGT-gapped germline V segment nucleotide sequence
GERMLINE_IMGT_D_MASK string IMGT-gapped germline V(D)J nucleotide sequence with Ns masking the NP1-D-NP2 regions
GERMLINE_V_CALL string Clonal consensus germline V assignment
GERMLINE_D_CALL string Clonal consensus germline D assignment
GERMLINE_J_CALL string Clonal consensus germline J assignment
GERMLINE_REGIONS string Germline regions by position encoded as V, D, J, N, and P characters
DefineClones Annotations    
CLONE integer Numerical clone identifier of sample sequence
TIgGER Annotations    
V_CALL_GENOTYPED string Adjusted V allele assignment(s) following TIgGER genotype inference
pRESTO Annotations    
PRCONS string UMI consensus primer
PRIMER string list of primers
CONSCOUNT integer number of reads contributing to the UMI consensus sequence
DUPCOUNT integer copy number of the sequence