Plate Report
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A Plate Report is generated here. It contains some information and statistics about the data you have in your Plates. You can generate Reports for a single Plate or for all of them simultaneously.

A combo box allows the user to select the kind of Plate that is going to be used in the Report:

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Selecting All Plates will create a general Report including all plates together.

Selecting the option:
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you can choose see genotypes that were canceled during the Quality Control process that can be performed in the Quality Control/Coherence section.

The Report will be sent to the User Results section. It will have the following structure:

1. A header with general information about the plates used in the report:

Plate/s Information
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Plate      : SNPlex
Study      : sample 1
User       : advanced
Date       : 2005-08-04 17:14:32
Technology : SNPlex
Source     : Placa.txt

2. Overall statistics on the data:

Final Report
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Genotypes ....
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Unique genotypes               : 16225 (96.97%)
Empty genotypes                 : 461 (2.76%)
Concordant repetitions               : 46 (0.27%)
Non concordant repetitions       : 0 (0.00%)
Total genotypes                   : 16732
Total tested                          : 100.00 %
Total genotyped                   : 97.24 %

SNPs ....
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SNPs with more than two alleles  : 0(0.00%)
Total SNPs                       : 47

Samples ....
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Total samples                   : 356


Here a Genotype is defined as the combination of a Sample and a SNP. If several genotypes referring to the same Sample and SNP (as it would be the case if internal controls had been set up in the Plate), they are counted as a single genotype.

Keeping this in mind, the above categories stand for the following:

Unique genotypes:
Genotypes that have been uploaded once with a correct result (a valid genotype, e.g: AA, GT...).

The option:

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   allows the user to exclude Unique genotypes from the report.

Empty genotypes:
Genotypes that have been entered for which no correct result has been obtained. They usually correspond to failed tests in the plate.

Concordant repetitions:
These are genotypes that present more than one correct result, all of these results being  identical. This should be the case if internal control repetitions had been introduced in one or several plates.

Non concordant repetitions:
Genotypes that present more than one correct result. When checked, however, these results were found not to be identical. This situation alerts you of some kind of anomaly that has to be worked out in the Quality Control section. Otherwise, SNPator won't allow the Transfer of data from the Raw Genotypes table to the Genotypes table and no analysis will be possible.

Total genotypes:
The sum of all the above.

Total tested:
Genotypes that you have tested as a percentage of  all possible combinations of SNPs and Samples present in the plates. A genotype is considered tested even if no result came from it. This statistic only makes sense, of course, if you intended to test all combinations from a set of samples and SNPs (which is quite usual).

Total Genotyped:
Unique Genotypes + Concordant Genotypes as a percentage of Total Genotypes. Allows you to know the analytical success of your plate.

SNPs with more than two alleles:
SNPs whose genotypes include more than 2 alleles, expressed in absolute number and as a percentage of total SNPs.

Total SNPs:
Total SNPs that appear in the genotypes present in the plate(s) of the report.

Total Samples:
Total SNPs that appear in the genotypes present in the plate(s) of the report.

3. Detail of the above sections:

In case any problem is encountered, you can check the actual values of all the Genotypes, SNPs and Samples to which the above statistics made reference:

Unique genotypes
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5037016        SNPlex       sample 1   hCV2633914   HGDP00115    AG 
5034532        SNPlex       sample 1   hCV2633914   HGDP00116    AG 
5037070        SNPlex       sample 1   hCV2633914   HGDP00118    AA 
5034586        SNPlex       sample 1   hCV2633914   HGDP00119    GG     ...               

In the SNPs and Sample sections you have the individual percentage of genotyping success together with a simple graphical representation:


SNP List
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HCV2633914   99.45% |********* |
RS1013630    99.45% |********* |
RS1017672    99.45% |********* |
RS1035585    99.45% |********* |
RS10498529   99.45% |********* |
RS1054936    99.17% |********* |
RS12437400   99.45% |********* |
RS12579353   99.45% |********* | (GG) 
RS1325290    99.45% |********* |
RS1414482    99.45% |********* |
RS145527     99.45% |********* |
RS1519203    99.45% |********* |
RS1554326    99.17% |********* |
RS1555519    99.17% |********* |
RS2098787    99.45% |********* |
RS2193380     0.28% |          | (AT) 
RS2281305    99.45% |********* |
RS2286595    99.45% |********* |
RS2289942    99.45% |********* |


Here you can see that when a SNP presents the same genotype in all tests performed, that genotype is indicated.