gaps in consensus built from samtools pileup

[culmen]

thanks a lot for your reply.

The gaps means uncovered genomic positions. The sites without reads are not reported.

I do understand that sites without reads are not reported.

But when I view that portion in ensemble genome browser of 1000 genomes, I can see consensus bases and coverage at those locations as shown here. ( either there must be some way to get that consensus bases or that browser might be using some other data )

[luxmare]

The gaps means uncovered genomic positions. The sites without reads are not reported.

[culmen]

Hi,
I am a newbie to NGS data.

I was trying to extract consensus from BAM files of 1000genomedata (namely ftp://ftp-trace.ncbi.nih.gov/1000gen...e.20100125.bam 8:125807080-126007080) by samtools pileup consensus calling (ref: hg19 human_g1k_v37.fasta.gz )

I found some bases/positions like bases between position 125906527 and 125906541.

What might be the reason?
Can you guys please help me to obtains those missing bases?

Thanks a lot,
Culmen