bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/chain.html src/hg/htdocs/goldenPath/help/chain.html index e61db1634d4..c94bffad4a8 100755 --- src/hg/htdocs/goldenPath/help/chain.html +++ src/hg/htdocs/goldenPath/help/chain.html @@ -65,56 +65,56 @@ The alignment start and end positions are represented as zero-based half-open intervals. For example, the first 100 bases of a sequence would be represented with start position = 0 and end position = 100, and the next 100 bases would be represented as start position = 100 and end position = 200.

NOTE: When the strand value is "-",the query coordinates (qStart and qEnd) are on the reverse strand and must be subtracted from the chromosome size to obtain the correct position on the forward strand in the other genome. The reverse coordinates are subtracted as follows to get forward strand coordinates:

    qStartForward = qSize - qEnd 
     qEndForward   = qSize - qStart

For example, using the query coordinates from chain 5 in -hg38ToMm10.over.chain.gz: 

    chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id
     chain 442878230 chr1 248956422 + 158547112 207360161 chr1 195471971 - 21022354 65032227 5

The reverse strand coordinates are subtracted from the chromosome size:

    mm10Start = 195471971 - 65032227 = 130439744
     mm10End   = 195471971 - 21022354 = 174449617

The forward strand coordinates for chain 5 on mm10 are chr1 130439744 174449617, or with 1-based coordinates for a position range, chr1:130,439,745-174,449,617.

To reverse the calculation and derive the corresponding hg38 coordinates using chain 5 in -mm10ToHg38.over.chain.gz, note that the derived mm10 coordinates match the tStart and tEnd values:

    chain 442878230 chr1 195471971 + 130439744 174449617 chr1 248956422 - 41596261 90409310 5

The hg38 coordinates are subtracted as follows:

    hg38Start = 248956422 - 90409310 = 158547112
     hg38End   = 248956422 - 41596261 = 207360161

These coordinates match the target coordinates in -hg38ToMm10.over.chain.gz.

Alignment Data Lines

Alignment data lines contain three required attribute values:

    size dt dq