Warning while using mergeit

Hi,

using the mergeit tool, I'm getting the following output :

parameter file: merge1.txt
geno1: pop1.geno
snp1: pop1.snp
ind1: pop1.ind
geno2: pop2.geno
snp2: pop2.snp
ind2: pop2.ind
outputformat: EIGENSTRAT
genooutfilename: merged_files/merged.geno
snpoutfilename: merged_files/merged.snp
indoutfilename: merged_files/merged.ind
allele funny: rs3866853 C T C A
allele funny: rs186227113 T C T G
allele funny: rs76848438 G T T C
allele funny: rs571647631 T C T G
allele funny: rs536650371 C T C A
allele funny: rs569883333 G A G T
allele funny: rs533376218 A G A C
allele funny: rs12922580 T G T C
allele funny: rs540831825 A C A G
allele funny: rs536259035 G A G T
allele funny: rs7246683 T G G A
numsnps input: 22080043 38851429
eigenstrat output
numsnps output: 10100139 numindivs: 1164

Histogram of checkmatch return codes
kode: -1 2 X allele and strandcheck
kode: -2 1808577 A/T or C/G and strandcheck
kode: 0 11 Allele mismatch
kode: 1 9135811 SNP OK (no flip)
kode: 2 964328 SNP OK (flip)
total: 11908729

Over here,
--> what is exactly meant by 'allele funny' giving allele mismatch?
--> is the number of SNPs in the input files dropping from 20M and 30M to 10M in the output file, fine?

Thanks in advance!

Start with the mergeit entry point and the parameter file named merge1.txt, using the reported allele funny lines and SNP counts as the reproduction details. Trace where these messages and the input/output counts are produced, then document whether the warnings and reduction are expected; no source file or test is identified in the issue.