I use snpEff to annotate the snp result, but I found that the annotation of SNP wre not consistent with the SNP result.

e.g.:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT sample1
AL123456.3      11820   .       C       G       9080.29 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=260;CIGAR=1X;DP=261;DPB=261;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=365.042;PAIRED=0.992308;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10156;QR=0;RO=0;RPL=149;RPP=15.0703;RPPR=0;RPR=111;RUN=1;SAF=127;SAP=3.31097;SAR=133;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|alaT-Rv0008c|gene8-gene9|intergenic_region|gene8-gene9|||n.11820C>G||||||        GT:DP:RO:QR:AO:QA:GL    1/1:261:0:0:260:10156:-913.182,-78.2678,0
AL123456.3      11879   .       A       G       8225.32 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=236;CIGAR=1X;DP=237;DPB=237;DPRA=0;EPP=3.0471;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=331.771;PAIRED=0.991525;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9203;QR=0;RO=0;RPL=99;RPP=16.2968;RPPR=0;RPR=137;RUN=1;SAF=118;SAP=3.0103;SAR=118;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0008c|gene9|transcript|TRANSCRIPT_gene9|protein_coding|1/1|c.433T>C|p.Ser145Pro|433/438|433/438|145/145||  GT:DP:RO:QR:AO:QA:GL    1/1:237:0:0:236:9203:-827.719,-71.0431,0

As in the example, line 3 the original SNP was A->G at the position of 11879 in AL123456.3, while the snpEff annotated result show that c.433T>C, which means the variant occurred in the CDS of Rv0008c (at the position of 433 bp of the CDS and the alternation was T->C).

I wonder why the annotation of variant was not identical with the snp. Besides, this question did not occurred in the first annotated snp.