[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
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