How is the phasing done in single sample HaplotypeCaller?

Hi, after running HaplotypeCaller with this commands
gatk --java-options "-Xmx4g" HaplotypeCaller -R $refGenome -I /home/ready.bam -ERC GVCF -O /home/GATK4-HC.g.vcf

I obtain positions in the gvcf file like these:
1 1243896 . C T, 0.01 . MLEAC=0,0;MLEAF=NaN,NaN GT ./.
1 1243929 . G T, 0.01 . MLEAC=0,0;MLEAF=NaN,NaN GT:PGT:PID ./.:0|1:1243929_G_T
1 4204648 . CTACCA C, 0 . MLEAC=0,0;MLEAF=NaN,NaN GT:PGT:PID ./.:0|1:4204601_T_C
1 6292991 . C . . END=6293126 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0

How is possible that those positions have 0|1 if I have not used any database nor any other samples?

How is ./. different of 0/0:0:0:0:0,0,0 in the GT field?

Thank you very much

Answers

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