Missing FASTQ files in European 1KGP trio?

[gene coder]

I think that some FASTQ files containing exome reads from the European trio in the 1KGP project are missing.

Read groups in an exome file (NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam):

daggy@daggy-Studio-XPS-8100:~/Downloads$ samtools view -H NA12878/exon/NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam
...
@RG     ID:SRR013620    PL:ILLUMINA     LB:Solexa-5324  PI:0    DS:SRP000033    SM:NA12878      CN:BI
@RG     ID:SRR013890    PL:ILLUMINA     LB:Solexa-7288  PI:0    DS:SRP000033    SM:NA12878      CN:BI
@RG     ID:SRR014820    PL:ILLUMINA     LB:Solexa-10292 PI:300  DS:SRP000033    SM:NA12878      CN:BI
@RG     ID:SRR015370    PL:ILLUMINA     LB:2773962043   PI:0    DS:SRP000033    SM:NA12878      CN:WUGSC
@RG     ID:SRR016607    PL:ILLUMINA     LB:Solexa-11435 PI:201  DS:SRP000033    SM:NA12878      CN:BI
@RG     ID:SRR017279    PL:ILLUMINA     LB:Solexa-7288  PI:0    DS:SRP000033    SM:NA12878      CN:BI

If you take a look at the FASTQ raw reads, you will find all read groups but SRR013620 for NA12878. For NA12891, the read group SRR013888 is missing; and for NA12892, SRR013619. The African trio (NA19238-40) is OK.

But the reads in read group SRR013620 are present in the BAM file:

daggy@daggy-Studio-XPS-8100:~/Downloads$ samtools view NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam | grep SRR013620 | wc
 142742 3118113 41310387

After searching on Google, I found the read group SRR013620 at an EBI site.

The files at the 1KGP FTP site are filtered ("filt" in the file names). Those at the EBI site do not have that substring suggesting that they are unfiltered. A comparison of the files SRR013890.filt.fastq.gz and SRR013890/SRR013890.fastq.gz shows that the 1KGP is smaller (294 MB vs 303 MB), confirming the hypothesis.

I found in another thread the sequence index file of 1KGP that the md5sum is missing (described here), suggesting that the missing FASTQ files are not supposed to exist.

Can anybody tell me what is going on here? Are some FASTQ files missing, or located somewhere else? Can I use the FASTQ files at the EBI site, and do they have lower quality if unfiltered?