GATK BaseRecalibration report

Question

[stephenn]

hi everyone

I use GATK to do snp call. But I don't understand the BaseRecalibration report as follows . And I really don't known the word 'Observations' 'Errors' stand for.

Thanks in advance

RaedGroup            R11               R11               R11
EventType            M                  I                 D
EmpiricalQuality     15.0              28.0               26.0
EstimatedQReported    32               45                  45
Observations         1.23e+08     1.23e+08               1.23e+08
   Errors            4.35e+06      2.15E+05             4.28e+05

Answer 1

[hosgroupcp2]

me to :(

i really don't known the word 'Observations' 'Errors' stand for.

Thanks in advance

RaedGroup            R11               R11               R11
EventType            M                  I                 D
EmpiricalQuality     15.0              28.0               26.0
EstimatedQReported    32               45                  45
Observations         1.23e+08     1.23e+08               1.23e+08
   Errors            4.35e+06      2.15E+05             4.28e+05

Answer 2

[hosgroupcp2]

Observational error (or measurement error) is the difference between a measured value of quantity and its true value. In statistics, an error is not a "mistake". Variability is an inherent part of things being measured and of the measurement process.

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