Complete Documentation#

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H2M Output Data Description#

Column Description
0 gene_name_h Human gene name
1 gene_id_h Human gene ID
2 tx_id_h Human transcript ID
3 chr_h Human chromosome number
4 exon_num_h Total number of exons of the human transcript
5 strand_h Positive or Negative strand of the human transcript on the chromosome
6 match The computed reference sequence by given coordinate is matched with the input reference sequence or not
7 start_h | end_h Start and end position of the human variant on the chromosome in MAF format
8 ref_seq_h | alt_seq_h Reference and alternate sequence of the human variant on the chromosome in MAF format
9 HGVSc_h | HGVSp_h HGVSc and HGVSp expression of the human variant
10 classification_h Human variant effect classification, including missense/nonsense/in-frame indel/fram-shift indel/intron, etc.
11 exon_h Exon/Intron location of the given human mutation, for example, E_7/I_5
12 type_h Human variant type in MAF format, including SNP/DNP/TNO/ONP/INS/DEL
13 status This mutation can be modeled in the given target transcript or not, True or False
14 class H2M modeling result class, 0-5
15 statement Statement of the H2M result class
16 flank_size_left | flank_size_right Length of the identical sequences between human and mouse on the left/right side of the mutation
17 gene_name_m Mouse gene name
18 gene_id_m Mouse gene ID
19 tx_id_m Mouse transcript ID
20 chr_m Mouse chromosome number
21 exon_num_m Total number of exons of the mouse transcript
22 strand_m Positive or negative strand of the mouse transcript on the chromosome
23 type_m Mouse variant type in MAF format, including SNP/DNP/TNO/ONP/INS/DEL
24 classification_m Mouse variant effect classification
25 exon_m Exon/Intron location of the murine mutation
26 start_m_ori | end_m_ori Start and end position of the mouse variant (with exactly the same DNA change) on the chromosome in MAF format
27 ref_seq_m_ori | alt_seq_m_ori Reference and alternate sequence of the mouse variant (with exactly the same DNA change) on the chromosome in MAF format
28 HGVSc_m_ori | HGVSp_m_ori HGVSc and HGVSp expression of the mouse variant (with exactly the same DNA change)
29 start_m | end_m Start and end position of the mouse variant (with the same amino acid change) on the chromosome in MAF format
30 ref_seq_m | alt_seq_m Reference and alternate sequence of the mouse variant (with the same amino acid change) on the chromosome in MAF format
31 HGVSc_m | HGVSp_m HGVSc and HGVSp expression of the mouse variant (with the same amino acid change)

H2M Modeling Class Description#

Class Statement
0 Class 0 This mutation can be originally modeled.
1 Class 1 This mutation can be alternatively modeled.
2 Class 2 This mutation can be modeled, but the effect may not be consistent.
3 Class 3 This mutation cannot be originally modeled and no alternative is found.
4 Class 4 Mutated sequences are not identical.
5 Class 5 Coordinate error. This mutation is not in the query gene.
6 Class 6 This mutation cannot be originally modeled.

Functions#