[ensembl-dev] SQL sentence gets variation inconsistent with API result

陈岗 danielchen06 at gmail.com
Tue Aug 14 10:17:05 BST 2012


Hi All

I got variation IDs with SQL sentences, but their numbers are inconsistent
with the result from API.

For example, my SQL counts gene ENSG00000089234 has 38 insertions, 45
deletions, 5 indels, 0 substitution. However, Ensembl API read out 30
insertions, 40 deletions 1 substitutions.

If anyone know the reason that causes the difference, please tell me.
 Thanks

My SQL  for insertion:

( SELECT att.value,vf.variation_name
FROM transcript_variation tv
LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id )
LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id )
WHERE tv.feature_stable_id = 'ENST00000419234'
     AND att.value = 'insertion' )

union

( SELECT att.value,vf.variation_name
FROM transcript_variation tv
LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id )
LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id )
WHERE tv.feature_stable_id = 'ENST00000327551'
     AND att.value = 'insertion' )

union

( SELECT att.value,vf.variation_name
FROM transcript_variation tv
LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id )
LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id )
WHERE tv.feature_stable_id = 'ENST00000547043'
     AND att.value = 'insertion' )

union

( SELECT att.value,vf.variation_name
FROM transcript_variation tv
LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id )
LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id )
WHERE tv.feature_stable_id = 'ENST00000539060'
     AND att.value = 'insertion' )


-- 
Gang Chen
TILSI
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
P.R.China
Phone:(+86)512-82782588
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120814/2e75edf7/attachment.html>


More information about the Dev mailing list