SSM Affected Cases in Cohort from DNA mutation of TCGA data portal
Hi All,
I am a little confused about how to understand the mutation information from mutation data of the TCGA data portal.
Take SMARCB1 as an example,
127 cases have SMARCB1 mutation 10202 is totally TCGA cohort samples.
Who can explain what's 705 and 751 in the figure?
Thanks.
ssm
tcga
mutation
smarcb1
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Zhenyu Zhang
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