How Do I Interpret The Output Generated By Variationhunter?

Question

[Bioscientist]

I'm using Variationhunter to analyze CNV; and when I used hg18 reference genome sometime ago, I usually got the output as:

IL5_286:1:311:10:40    chr1    142188880    142188915    R    141736787    141736822    F    deletion    3    23.930555    0.00257801939733326435
IL5_286:1:317:831:353    chr16    28530262    28530297    R    28517264    28517299    F    deletion    0    26.263889    1.00000000000000000000

The second column tells at which chromosome the potential CNV lies.

Now when I switch to humang1kv37.fasta (one version of hg19), I get output like below:

HWI-ST150_0129:3:47:9776:140941    1 dna:chromosome chromosome:GRCh37:1:1:249250621:1    144308983    144309081    F    143689458    143689556    F    V    4    60    2.254486e-12
HWI-ST150_0129:3:4:4776:183027    GL000225.1 dna:supercontig supercontig::GL000225.1:1:211173:1    6803    6901    F    102087    102185    F    V5    64    1.502623e-12

We can see the format difference is: where used to be "chr#" is replaced by three columns as "1 dna:chromosome chromosome:GRCh37:1:1:249250621:1"

So what's this "1 dna:chromosome chromosome:GRCh37:1:1:249250621:1"? Is it a header indicating chromosome # or sth? Also I can grep this "header" from humang1kv37.fasta; but seems human_hg18.fastq doesn't contain such header-like stuff.

Also "L000225.1 dna:supercontig supercontig::GL000225.1:1:211173:1" is quite confusing to me. What does "L000225.1" standard for? Some unusual part of chromosome? (like mitonchondrial chromosome?)

Thanks a lot.

Answer 1

[Bert Overduin]

chromosome:GRCh37:1:1:249250621:1

means that the sequence is

• a chromosome
• from the GRCh37 assembly
• chromosome number 1
• from basepair 1
• until basepair 249250621
• forward strand

in other words, the complete chromosome 1

GL000225 is a supercontig representing a dna sequence of which we don't know where it fits into the assembly. See also EMBL-Bank or GenBank.

Note that there also are supercontigs that represent alternate haplotypes e.g. GL000255.