Ok! this is what an SNP looks like!
contig_100029 698 C 39 .$.....,.,,,,.,,,.,.,..,......,,,,,,.,,^S.
contig_100029 699 A 38 .....,.,,,,.,,,.,.,..,......,,,,,,.,,.
contig_100029 700 A 38 .....,.,,,,.,,,.,.,..,......,,,,,,.,,.
contig_100029 701 C 39 TTTTTtTttttTtttTtTtTTtTTTTTTttttttTttT^ST
contig_100029 702 A 40 .....,.,,,,.,,,.,.,..,......,,,,,,.,,..^S,
contig_100029 703 G 41 .....,.,,,,.,,,.,.,..,......,,,,,,.,,.,.,
contig_100029 704 G 42 .....,.,,,,.,,,.,.,..,......,,,,,,.,,.,.,^S.
I have ommited the last column (read base qualities).
And what about a reference skip? Maybe want to see an spliced alignment? Here you are!
contig_100029 516 T 43 ,,,.,,...,.,,.................,.,,,,.,,,.,^S.
contig_100029 517 A 43 ,,,.,,...,.,,.................,.,,,,.,,,.,.
contig_100029 518 G 43 ,,,.,,...,.,,.................,.,,,,.,,,.,.
contig_100029 519 A 43 ,,,.,,...,.,,.................,.,,,,.,,,.,.
contig_100029 520 G 43 ,,,.,,...,.,,.................,.,,,,.,,,.,.
contig_100029 521 G 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 522 T 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 523 G 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 524 A 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
contig_100029 651 C 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 652 A 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 653 G 43 <<<><<>>><><<>>>>>>>>>>>>>>>>><><<<<><<<><>
contig_100029 654 G 44 ,,,.,,...,.,,.................,.,,,,.,,,.,.^S,
contig_100029 655 G 44 ,,,.,,..$.,.,,............$.....,.,,,,.,,,.,.,
contig_100029 656 C 42 ,,,.,,..,.,,................,.,,,,.,,,.,.,
contig_100029 657 G 42 ,,,.,,..,.,,................,.,,,,.,,,.,.,
Who wants an IGV when you can scroll up and down seeing how things pile down and up?
An it is memory efficient, right?
You just have to grep or awk filter your region of interest!
Do you want me to explain about columns?
An it is memory efficient, right?
You just have to grep or awk filter your region of interest!
Do you want me to explain about columns?
1st: reference_name
2nd: position in reference
3rd: base on reference
4th: depth, or number of bases pilling-up over this reference position
5th: each symbol comes from a read, with some exceptions. Lets look at it:
"." and ",": matches! one in fwd strand, "," in reverse.
"$": end of read. Followed by mapping symbol of that read base ("." or "," for example). So, 2 symbols.
"^": start of read. Followed by mapping quality of the read (the MAPQ field in SAM format) and the mapping symbol of that base ("." or "," for example).
">" "<": reference skip. That is, the read still maps, but no in these reference bases. So probably an spliced alignment with part of the read aligning before the ">" and part after that. ">" fwd strand, "<" reverse.
6th: (not shown, just working with HQ bases ;)
6th: (not shown, just working with HQ bases ;)
Looking for more information? Ask please!
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