I am using impute2 to impute the genotype of a GWAS data with two reference panels, 1000GP and a WGS panel.

impute2 -use_prephased_g -m genetic_map_chr22_combined_b37.txt -h 1000GP_Phase3_chr22.hap.gz wgs_chr22.impute.hap -l 1000GP_Phase3_chr22.legend.gz wgs_chr22.impute.legend -int 45000001 5e+07 -buffer 500 -known_haps_g gwas_chr22.haps.gz -o chr22.set10_seq.gprobs -i chr22.set10_seq.metrics -os 0 2 -o_gz -verbose

The "data processing" says, for panel 1 (WGS), impute2 "reads 66404 SNPs in the analysis interval+buffer region --excluded 60027 SNPs, leaving 6377 SNPs for analysis."

But in the "data summary", it says "0 type 1 SNPs."

Does "type 1" refer to SNP in Panel 1 ONLY? Does it mean that Panel 1 does not contribute to the imputation? The 6377 SNPs all go into the "5439 type 2 SNPs" (SNP in Panel 2 and all ref panels)? I appreciate any suggestions.

-------------
 Input files
-------------

         Panel 0 haplotypes: 1000GP_Phase3_chr22.hap.gz
         Panel 0 hap legend: 1000GP_Phase3_chr22.legend.gz
         Panel 1 haplotypes: wgs_chr22.impute.hap
         Panel 1 hap legend: wgs_chr22.impute.legend
         Panel 2 known haps: gwas_chr22.haps.gz
                genetic map: genetic_map_chr22_combined_b37.txt

-----------------
 Data processing
-----------------

-reading genetic map from -m file
 --filename=[genetic_map_chr22_combined_b37.txt]
 --read 10367 SNPs in the analysis interval+buffer region

-reading Panel 2 haplotypes from -known_haps_g file
 --filename=[gwas_chr22.haps.gz]
 --detected 3688 individuals
 --read 7232 SNPs in the analysis interval+buffer region
 --updated 11 existing SNPs with known haplotype info
 --added 7221 new SNPs based on known haplotypes
   --4 of these replace existing SNPs with incompatible alleles

-reading Panel 1 haplotypes from -h and -l files
 --filename=[wgs_chr22.impute.hap]
 --filename=[wgs_chr22.impute.legend]
 --detected 198 haplotypes
 --read 66404 SNPs in the analysis interval+buffer region
 --excluded 60027 SNPs, leaving 6377 SNPs for analysis

-reading Panel 0 haplotypes from -h and -l files
 --filename=[1000GP_Phase3_chr22.hap.gz]
 --filename=[1000GP_Phase3_chr22.legend.gz]
 --detected 5008 haplotypes
 --read 228896 SNPs in the analysis interval+buffer region

-removing SNPs that violate the hierarchical data requirements
 --converted 657 genotyped SNPs with ref panel data to type 3 (these will not inform the imputation)

-removing reference-only SNPs from buffer region
 --removed 34209 SNPs

-checking strand alignment between Panel 1 and Panel 0 by allele labels
 --flipped strand due to allele mismatch at 0 out of 6357 SNPs in Panel 1

-checking strand alignment between Panel 2 and Panel 0+1 by allele labels
 --flipped strand due to allele mismatch at 1935 out of 6357 SNPs in Panel 2

-aligning allele labels between panels

-removing non-aligned genotyped SNPs
 --removed 0 out of 6357 SNPs with data in multiple panels

--------------
 Data summary
--------------

[type 0 = SNP in Panel 0 only]
[type 1 = SNP in Panel 1]
[type 2 = SNP in Panel 2 and all ref panels]
[type 3 = SNP in Panel 2 only]

-Upstream buffer region
 --0 type 0 SNPs
 --0 type 1 SNPs
 --689 type 2 SNPs
 --0 type 3 SNPs
 --689 total SNPs

-Downstream buffer region
 --0 type 0 SNPs
 --0 type 1 SNPs
 --229 type 2 SNPs
 --0 type 3 SNPs
 --229 total SNPs

-Analysis region (as defined by -int argument)
 --187693 type 0 SNPs
 --0 type 1 SNPs
 --5439 type 2 SNPs
 --0 type 3 SNPs
 --193132 total SNPs

-Output file
 --187693 type 0 SNPs
 --0 type 1 SNPs
 --5439 type 2 SNPs
 --0 type 3 SNPs

-In total, 194050 SNPs will be used in the analysis, including 6357 Panel 2 SNPs