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  • GeneMapper v4.0

    Getting Started Guide

  • GeneMapper v4.0

    Getting Started Guide

  • ii GeneMapper Software Version 4.0 Getting Started Guide

    Copyright 2005, Applied Biosystems.All rights reserved.

    Applied Biosystems Applied Biosystems

    :

    Applera Corporation

    GeneMapper HID GeneMapper HID

    :ABI PRISM, Applied Biosystems, GeneMapper, GeneScan, LIZ and SNaPshot are registered trademarks and AB(Design), Applera GeneMapper, GeneScan and SNPlex are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.

    This product includes software developed by the Apache Software Foundation (http://www.apache.org/). Copyright 1999-2000

    The Apache Software Foundation. All rights reserved.

    This product includes software developed by the ExoLab Project (http://www. exolab.org/). Copyright 2000 Intalio Inc. All

    rights reserved.

    JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., http://www.trustice.com.

    Oracle is a registered trademark of Oracle Corporation.

    All other trademarks are the sole property of their respective owners.

    Applera Corporation is committed to providing the worlds leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses.

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    GeneMapper v3.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

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    Table Settings . . . . . . . . . . . . . . . . . . . . . . . . . 14

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    Auto Bin Bin Set Bin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

    3 33Analysis Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

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    GeneMapper Software Version 4.0 Getting Started Guide iii

  • iv GeneMapper Software Version 4.0 Getting Started Guide

  • GeneMapper Software Version 4.0 Getting Started Guide Applied Biosystems Data Collection GeneMapper

    GeneMapper

    GeneMapper Software Version 4.0 Installation and Administration Guide(PN 4363080)GeneMapper v4.0

    Microsoft Winows XP

    0 [Enter]

    File Open Spot Set

    View Filter View All Runs

    Applied Biosystems 2

    Control Console

    GeneMapper Software Version 4.0 Getting Started Guide v

  • Oracle ID

    1 96 1 Sample Entry

    GeneMapper Software v4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software v4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software 4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software v4.0 Installation and Administration Guide GeneMapper v4.0

    GeneMapper Software v4.0 Getting Started Guide GeneMapper 5 Applied Biosystems DataCollection LOHAFLP SNaPshot SNPlex GeneMapper

    GeneMapper Software v4.0 Online Help GeneMapper [F1]Help Contents and IndexGeneMapper 3

    GeneMapper Software v4.0 Quick Reference Guide GeneMapper

    GeneMapper Software v4.0 Reference and Troubleshooting Guide

    PDF GeneMapper Software v4.0 Documentation CD

    vii

    GeneMapper [F1] Help Contents and IndexGeneMapper 3

    vi GeneMapper Software Version 4.0 Getting Started Guide

  • Applied Biosystems

    jptechsupport@appliedbiosystems.com

    http://www.appliedbiosystems.co.jp Customer Support

    FAQ

    Applied Biosystems MSDSCertification of Analysis

    PDF

    Applied Biosystems

    GeneMapper Software Version 4.0 Getting Started Guide vii

    mailto:techpubs@appliedbiosystems.comhttp://www.appliedbiosystems.com

  • viii GeneMapper Software Version 4.0 Getting Started Guide

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    GeneMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

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    GeneMapper v3.7 . . . . . . . . . . . . . . . . . 5

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

    GeneMapper Software Version 4.0 Getting Started Guide 1

  • 1

    STR DNA 1 2 7 1

    PCR PCR GeneMapper

    Applied Biosystems PCR Applied Biosystems Web www.appliedbiosystems.co.jp

    Applied Biosystems GeneMapper Software Version 4.0 Quick Reference Guide(PN 4362816)

    2 GeneMapper Software Version 4.0 Getting Started Guide

  • 1

    3 .fsa

    :\AppliedBiosystems\GeneMapper\Example Data\Microsatellite

    GeneMapper D

    PCR GeneScan 500 LIZABI PRISM 3100

    17

    2 Panel Marker

    bp

    D6S264 Blue 108 130

    D6S1574 Blue 146 172

    D6S276 Blue 201 233

    D5S408 Blue 240 285

    D6S308 Blue 326 354

    D6S287 Green 104 138

    D6S292 Green 154 176

    D6S434 Green 201 245

    D5S426 Green 274 298

    D5S1981 Yellow 112 125

    D6S257 Yellow 167 195

    D6S446 Yellow 212 234

    D5S641 Yellow 299 339

    D5S433 Red 69 99

    D5S406 Red 168 196

    D5S400 Red 221 243

    D6S309 Red 307 333

    GeneMapper Software Version 4.0 Getting Started Guide 3

  • 1

    GeneMapper

    GeneMapper

    ( 4 )

    ( 2 )

    1. KitPanelMarker

    2.

    3. Table Settings

    4.

    5. Bin Set Bin Auto Bin

    ( 3 )

    1. Analysis Method Bin Set

    2.

    3.

    Analysis MethodSize StandardPanel GeneMapper

    Bin

    Marker bpBinMarker

    Bin Set

    Bin ) BinSet

    Marker

    bp

    Panel

    Marker GeneMapper Panel Bin SetMarker Bin

    Kit

    Panel

    4 GeneMapper Software Version 4.0 Getting Started Guide

  • 1

    GeneMapper

    1.StartAll ProgramApplied BiosystemsGeneMapperGeneMapper4.0

    2.Login to GeneMapper

    a.

    b.OK

    GeneMapper

    Software Online Help

    GeneMapper v3.7 GeneMapper v3.7

    GeneMapper v3.7 GeneMapper v3.7

    GeneMapper Software Version 4.0 Getting Started Guide 5

  • 1

    GeneMapper

    GeneMapper 2 GeneMapper Data Collection GeneMapper Version 4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper 2 GeneMapper GeneMapper Version 4.0 Installation and Administration Guide(PN 4363080)

    6 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    2

    4

    3

    1

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

    KitPanelMarker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

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    Table Settings . . . . . . . . . . . . . . . 14

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    Auto Bin Bin Set Bin . . . . . . . . . . . . . . . . . . . . . . . . . . 25

    GeneMapper Software Version 4.0 Getting Started Guide 7

  • 2

    KitPanelMarker

    Display Settings

    AutoBin Bin Set Bin

    GeneMapper GeneMapper Software Online Help

    Creating a New Kit Kit )

    Creating a Custom Panel )

    Creating MarkersMarker )

    Creating a Project )

    Adding Samples )

    Applying Analysis SettingsAnalysis Settings )

    Starting Analysis )

    Creating a New Bin SetBin Set )

    Using the Auto Bin FunctionAuto Bin )

    Help [F1]

    8 GeneMapper Software Version 4.0 Getting Started Guide

  • 2KitPanelMarker

    KitPanelMarker

    Panel Manager

    Kit Panel

    Panel Marker

    Marker bp

    Panel Marker Marker Panel AppliedBiosystems Linkage Mapping SetGeneMapper Panel Panel GeneMapper Software Online Help

    KitPanelMarker

    KitPanelMarker

    1. Panel Manager Tools Panel Manager

    2. Panel Manager File New Kit

    3.New Kit Kit Name Microsatellite Kit Kit Type Microsatellite OK

    GeneMapper Software Version 4.0 Getting Started Guide 9

  • 2KitPanelMarker

    Microsatellite Kit

    4. Microsatellite Kit FileNew Panel

    5. Panel Manager New Panel Panel Name Microsatellite Panel Enter

    Microsatellite Kit Microsatellite Panel

    6. Microsatellite Panel File New Marker

    7. Panel Manager Marker

    10 GeneMapper Software Version 4.0 Getting Started Guide

  • 2KitPanelMarker

    8. 6 7 Marker

    9. Panel Manager OK

    12 .fsa

    Marker Dye Color Minimum Size (bp) Maximum Size (bp)

    Marker Repeat

    D6S1574 Blue 146 172 2

    D6S276 Blue 201 233 2

    D5S408 Blue 240 285 2

    D6S308 Blue 326 354 2

    D6S287 Green 104 138 2

    D6S292 Green 154 176 2

    D6S434 Green 201 245 2

    D5S426 Green 274 298 2

    D5S1981 Yellow 112 125 2

    D6S257 Yellow 167 195 2

    D6S446 Yellow 212 234 2

    D5S641 Yellow 299 339 2

    D5S433 Red 69 99 2

    D5S406 Red 168 196 2

    D5S400 Red 221 243 2

    D6S309 Red 307 333 2

    GeneMapper Software Version 4.0 Getting Started Guide 11

  • 2

    GeneMapper

    Project

    Project

    1. File New Project

    2.New Project Microsatellite OK

    3.GeneMapper File Add Samples to Project

    4.Add Samples to Project Files

    :\AppliedBiosystems\GeneMapper\Example Data

    GeneMapper D

    5. Microsatellite Add to ListAdd

    Microsatellite 3 2 [Ctrl] Add To List

    12 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    Microsatellite 3 Applied Biosystems Data Collection Samples

    14

    GeneMapper Software Version 4.0 Getting Started Guide 13

  • 2 Table Settings

    Table Settings

    GeneMapper

    Analysis MethodBin Set

    PanelMarker ) Size Standard

    GeneMapper

    Table Settings Plot Settings

    1.GeneMapperSamples

    2.Analysis Method NewAnalysis Method

    GeneMapper Manager Analysis Method

    3.New Analysis Method Analysis Type Microsatellite OK

    14 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 Table Settings

    4.Analysis Method Editor 5

    General NameMicrosatellite Analysis Method

    Allele Bin Set None

    GeneMapper Software Version 4.0 Getting Started Guide 15

  • 2 Table Settings

    Peak Detector Peak Detection Algorithm Basic

    Peak Quality Process Quality ValuesPQV (Pass) (Check)

    Homozygous min peak height 140.0

    Heterozygous min peak height 85.0

    Min peak height ratio 0.4

    16 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 Table Settings

    Quality Flags

    Process Quality Values (PQV) Genotype Quality (GQ) PQV 0 1 0 1

    Sizing Quality (SQ GQ Pass Check Low Quality SQ GQ 1 PQV 1 SQ GQ

    Analysis Method GeneMapper Software Online Help

    5.OK Analysis Method Analysis Method Editor

    GeneMapper Software Version 4.0 Getting Started Guide 17

  • 2 Table Settings

    6.Panel Select a Panel Microsatellite Kit Microsatellite Panel 9

    7.Size Standard GS500(-250)LIZ

    GeneMapper GeneScan 500 LIZ

    GS500LIZ GeneScan 500 LIZ

    GS500(-250)LIZ 250-bp GS500LIZ_3730 35-250-340-bp GS500LIZ_3130 35-250-340-bp

    1 35-bp 250-bp 340-bp GeneMapper Software Online Help

    8.Samples

    a. Analysis MethodPanelSize Standard 3

    b.Edit Fill Down[Ctrl] [D]

    Microsatellite Kit

    18 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 Table Settings

    Table Settings

    GeneMapperTable Settings Microsatellite Default

    Table Settings SamplesGenotypes Microsatellite Default GeneMapper Table Settings 1

    GeneMapper Manager Table Settings GeneMapper Software Online Help

    1. File Save Project

    2.Save Project Microsatellite Project OK

    GeneMapper Microsatellite Project

    20

    GeneMapper Software Version 4.0 Getting Started Guide 19

  • 2

    Panel GeneMapper Analysis Method Bin Set GenotypeQuality (GQ)

    SQ PQV

    Raw Data

    Analysis Analyze

    GeneMapper GeneMapper

    SQ PQV Size Quality (SQ) Process Quality ValuePQV

    1.GeneMapper Analysis Completed

    2.SamplesSQ

    SQ (Pass) SQSFNFMNFSNFOS PQV

    SQ

    20 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    SQ

    SQ (Check) (Low Quality) PQVSFNFMNFSNFOS 21

    SQ Samples SQ

    1.Edit Select AllSamples

    2. Size Match Editor Analysis Size Match Editor

    2-1 Size Match Editor Size Matches

    3.Size Matches

    Size Quality (SQ)

    4. Sizing Quality 2-1 SQ (Pass) (Check) (LowQuality)

    Sizing Quality > 0.75 SQ (Pass)

    Sizing Quality SQ (Check)(Low Quality) 22 2-1

    5.

    2-1

    22 2-1

    Size Quality (SQ)

    GeneMapper Software Version 4.0 Getting Started Guide 21

  • 2

    6.Size Calling Curve

    7. Size Match Editor 3 6

    8.OKSize Match Editor

    GeneMapper SoftwareReference and Troubleshooting Guide

    Raw Data InfoRaw Data

    2-1

    Sizing Quality SQ (Check) (Low Quality)

    Size MatchesOverride SQSizing Quality 2-1Sizing Quality 1.0

    Size Matches Apply GeneMapper Software Online Help

    GeneMapper Software Online Help

    Raw Data

    22 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    1.View SamplesSamples

    2.Samples [Shift] [Ctrl] EditSelect All

    3. Analysis Display Plots

    Samples Plot

    4. Plot Setting Microsatellite Default

    Plot Settings Samples Plot Microsatellite Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help

    5. Samples Plot X Y

    X

    X [Shift]

    Zoom ToOK

    Y

    Y Zoom ToApply to all electropherogramsOK

    X Y

    X Y Full View

    Plot Setting Microsatellite Default

    X -

    GeneMapper Software Version 4.0 Getting Started Guide 23

  • 2

    Samples Plot

    Samples Plot

    X )

    Y

    Sizing

    Genotypes

    Sizing

    24 2-2

    [F1] GeneMapper Software OnlineHelp

    Samples Plot

    25 Auto Bin Bin Set Bin

    2-2 Samples Plot

    Sizing

    Sizing

    Sizing

    [Ctrl] [Shift]

    : Sizing [Ctrl] [G] Sizing

    24 GeneMapper Software Version 4.0 Getting Started Guide

  • 2Auto Bin Bin Set Bin

    Auto Bin Bin Set Bin

    Panel Manager Bin Set Bin

    Bin Set Kit Kit Kit Panel Bin Set

    Bin Panel Bin Set Panel Bin Panel Bin Panel Marker Bin Set

    Auto Bin Bin Bin Bin Set Bin Bin Set Bin GeneMapper Software Online Help

    Bin Set Bin Set

    1. Panel Manager Tools Panel Manager

    2. 9 Microsatellite Kit

    3. Bins New Bin Set

    4.New Bin Set Bin Set Name Microsatellite Bin Set OK

    Panel Manager Bin Set Microsatellite Bin Set Microsatellite Bin Set Microsatellite Panel Microsatellite Kit Panel

    GeneMapper Software Version 4.0 Getting Started Guide 25

  • 2Auto Bin Bin Set Bin

    PanelBin Set

    Microsatellite Panel Microsatellite Bin Set

    1.Bin Set Microsatellite Bin Set

    2. Microsatellite Kit 9 Microsatellite Panel

    Marker Panel Manager 27 2-3

    3. Bins Add Reference Data

    Add Microsatellite Reference Data Microsatellite Project

    Panel

    12

    Microsatellite

    Project

    26 GeneMapper Software Version 4.0 Getting Started Guide

  • 2Auto Bin Bin Set Bin

    4. Microsatellite Project Microsatellite Add to ListAdd

    Microsatellite Project Microsatellite Panel Panel Manager 27 2-3

    2-3 Panel Marker PanelManager

    Auto Bin Bin

    Auto Bin Bin

    1. Microsatellite Panel Bin Set Microsatellite Bin Set Bins Auto Bin

    2.Auto Bin

    Minimum quality value 0.1

    Allele Naming Scheme Number

    Auto Bin Options Auto Bin (clear existing bins)

    3.OK

    4.Autobinning completedOK

    5. Panel ManagerApply

    GeneMapper Software Version 4.0 Getting Started Guide 27

  • 2Auto Bin Bin Set Bin

    Marker Bin

    Marker Bin

    1. Microsatellite Panel Marker

    2-4

    Marker )

    Marker Bin

    Bin +

    2. Marker

    2-5

    Applied Biosystems Marker Marker Bin Bin GeneMapper Software Reference and Troubleshooting Guide

    2-4 Marker

    Markerbp

    Binbp bp

    Marker

    28 GeneMapper Software Version 4.0 Getting Started Guide

  • 2Auto Bin Bin Set Bin

    2-5 Marker

    Bin Set Bin Set Panel Manager OK

    Bin Marker

    Bin Marker Panel Manager Microsatellite Kit Microsatellite Panel

    Bin Marker Panel Manager Cancel OKApply

    Marker Bin

    1. Marker BinsAdd Bin

    2. Bin

    3.Add Bin Bin NameLocationOffsets OK

    Bin

    1. Bin

    2. Bins Edit Bin Bin EditBin

    3.Edit Bin Bin NameLocationOffsets OK

    Marker

    GeneMapper Software Version 4.0 Getting Started Guide 29

  • 2Auto Bin Bin Set Bin

    Bin

    1. BinBin 2-6

    2. Bin

    3. Bin

    Edit Undo

    2-6 Bin

    Bin

    Bin Marker

    Bin Bins Delete Bin

    Bin Bin Delete Bin

    Marker

    1. Marker 30 2-7

    2. Marker

    Edit Undo

    2-7 Marker

    Bin

    Bin

    Marker

    30 GeneMapper Software Version 4.0 Getting Started Guide

  • 2Auto Bin Bin Set Bin

    Panel Marker

    1. Marker

    2. Edit Clear Marker

    3

    GeneMapper Software Version 4.0 Getting Started Guide 31

  • 2Auto Bin Bin Set Bin

    32 GeneMapper Software Version 4.0 Getting Started Guide

  • 3

    3

    2

    1

    4

    Analysis Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

    GeneMapper Software Version 4.0 Getting Started Guide 33

  • 3Analysis Method

    Analysis Method

    14 Microsatellite Analysis Method Bin Set Bin Set Analysis Method Bin Set Bin Set GeneMapper

    Analysis Method

    Microsatellite Analysis Method

    1. GeneMapper Manager Tools GeneMapper Manager

    2.Analysis Methods

    3. Microsatellite Analysis Method Open

    34 GeneMapper Software Version 4.0 Getting Started Guide

  • 3Analysis Method

    4. Analysis Method Editor AlleleBin Set Microsatellite Bin SetOK

    5.Done GeneMapper Manager

    GeneMapperSamplesAnalysis MethodAnalysis Method Editor 14

    36

    GeneMapper Software Version 4.0 Getting Started Guide 35

  • 3

    Analysis Method Bin Set GeneMapper

    GeneMapperSamples

    Status SamplesMicrosatellite Analysis Method

    REF Bin Set

    Analysis Analyze

    GeneMapper GeneMapper

    36 GeneMapper Software Version 4.0 Getting Started Guide

  • 3

    SQ PQVSize Standard 20 24

    GQ PQV 37

    38

    Genotype Plot 38

    Genotypes Plot39

    39

    GQ PQV Genotype Quality (GQ) Genotypes

    GQ (Pass) GQ Process Quality Values (PQV)ANBDBINLPHOBAOSPHRSHPSPSPASPUXTLK

    GQ

    GQ (Check) (Low Quality) GQ PQVANBDBINCCLPHOBAOSPHRSHPSPSPASPUXTLK Marker Bin GeneMapper Software Reference and Troubleshooting Guide

    GQ Genotypes GQ

    GQ

    Genotypes

    GeneMapper Software Version 4.0 Getting Started Guide 37

  • 3

    Marker GenotypesAllele 1Allele 2

    Genotype Plot

    Genotypes Plot

    1.Genotypes Marker Marker [Shift] [Ctrl] Marker Edit Select All

    2. Analysis Display Plots

    Genotypes Plot Marker

    3. Plot Setting Microsatellite Default

    Plot Settings Genotypes PlotMicrosatellite Default GeneMapper PlotSettings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help

    Marker

    Plot Setting Microsatellite Default

    X -

    38 GeneMapper Software Version 4.0 Getting Started Guide

  • 3

    4. Genotypes Plot X Y

    Genotypes Plot

    Genotypes Plot

    X )

    Y

    Marker Bin

    [F1] GeneMapper Software OnlineHelp

    Genotypes Plot

    Marker

    1. Panel Manager Tools Panel Manager

    2. Microsatellite KitMicrosatellite Panel Marker

    3.Bins Show Project Alleles

    Y Marker GQ

    X

    X

    Zoom ToOK

    Y

    Y Zoom ToApply to all electropherogramsOK

    X Y

    X Y Full View

    GeneMapper Software Version 4.0 Getting Started Guide 39

  • 3

    40 GeneMapper Software Version 4.0 Getting Started Guide

  • 4

    4

    2

    1

    3

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

    GeneMapper Software Version 4.0 Getting Started Guide 41

  • 4

    File Print

    Report Settings GeneMapper Software Online Help

    / GeneMapper Project

    GeneMapper Samples

    View Samples

    GeneMapper Genotypes

    View Genotypes

    GeneMapper Info

    View Sample Info

    GeneMapper Raw Data

    View Raw Data

    GeneMapper EPT Data

    View EPT Data

    Samples Plot SamplesAnalysis Display Plots

    Genotypes Plot GenotypesAnalysis Display Plots

    Report Manager Analysis Report Manager

    42 GeneMapper Software Version 4.0 Getting Started Guide

  • 4

    SamplesGenotypes

    GeneMapperSamplesGenotypes

    1.

    a.GeneMapper Table Setting Table Setting

    b. EditSortSamplesGenotypes[Shift] Analysis Low Quality on TopGQ

    Table Settings GeneMapper Software Online Help

    2. 1

    File Export Table

    File Export Combined Table Samples

    Kit

    Panel Manager Kit

    1. Panel Manager Tools Panel Manager

    2.File Export All Kits

    Panel

    Kit Panel

    1. Panel Manager Tools Panel Manager

    2. Kit

    3.File Export Panels

    Bin Set

    Bin Set

    1. Panel Manager Tools Panel Manager

    2. Bin Set Kit

    3.Bin Set Bin Set

    4.File Export Bin Set

    GeneMapper Software Version 4.0 Getting Started Guide 43

  • 4

    ProjectSettingsSize Standard

    ProjectAnalysis MethodTable SettingsPlot SettingsReports SettingsSize Standard

    1. GeneMapper Manager Tools GeneMapper Manager

    2. 1 Projects

    Analysis Methods

    Table Settings

    Plot Settings

    Report Settings

    Size Standards

    3. [Shift] [Ctrl]

    4.Export

    Report Settings GeneMapper Software Online Help

    44 GeneMapper Software Version 4.0 Getting Started Guide

  • AAdvanced 16Analysis Method

    44 14 15, 35 34 17

    Analysis Method Editor

    Allele 15, 35General 15Peak Detector 16Peak Quality 16Quality Flags 17

    Applied Biosystems

    vii

    vii vii

    Auto Bin 27

    BBin

    Auto Bin 27Marker 29 28 30 25 4, 25 29

    Bin Set

    Analysis Method 15, 35 25 43 29 25 4, 25

    GGenotype

    QualityGQ

    Genotypes Plot 42 43 39 39

    38

    Genotypes 37

    Genotypes 24GQ

    37 37

    HHeterozygous min peak height 16

    Homozygous min peak height 16

    KKit

    43 9 9 4, 9 2

    MMarker

    Bin 29Panel 31 28 9 2, 4, 9 3, 11 38 30

    Min peak height ratio 16

    MSDS vii

    PPanel

    9 43 18 9 4, 9 26

    Panel Manager

    9Plot Setting 23, 38, 44PlotGenotypes Plot

    GeneMapper Software Version 4.0 Getting Started Guide 45

  • Samples Plot

    RReport

    42 44 44

    Report Settings 44

    SSamples Plot

    42 43 23 24 23

    Samples 14Size Match Editor 21

    Size Standard

    44 18 22 21 3 22 22 22 22

    Size Quality (SQ)

    SQ

    Sizing 24SQ

    22 20 21 21

    TTable Settings 14, 19, 44

    XX 23, 39 24, 39

    YY 23, 39 24, 39

    38

    39

    Genotypes Plot 42Report 42

    Samples Plot 42 42

    Bin Set 25Panel 9

    Analysis Method 44Bin Set 43

    Genotypes Plot 43Kit 43Panel 43Plot Settings 44Project 44Report 44Report Settings 44

    Samples Plot 43Size Standard 44Table Settings 44

    43

    vi

    7

    14 4, 14

    23, 39Genotypes Plot 39Samples Plot 23X 23, 39Y 23, 39

    vi

    24, 39 42 43

    46 GeneMapper Software Version 4.0 Getting Started Guide

  • v

    22

    Bin 30Marker 31

    22

    Analysis Method 14Bin 27Bin Set 25Kit 9Marker 9Panel 9Project 12Report 44

    23, 39 21, 37

    23, 39 22 21, 37 3 12 23, 38

    23, 39 23, 38

    23, 39

    20

    3 2

    5 4

    Marker Bin 29 22 12

    Size Standard 3

    3 3 3, 11

    vii

    vii

    16

    v v ! v v v v v v

    30

    18

    v

    2

    Table Settings 14 44 20, 36 14 12 12 19

    39

    20, 36

    vi

    GeneMapper Software Version 4.0 Getting Started Guide 47

  • Analysis Method 34Bin 29, 30Marker 30

    22

    Analysis Method 17

    19

    2 2 7 2 4 2

    v

    Analysis Method

    v

    v

    vii

    ii

    Panel 26 36

    48 GeneMapper Software Version 4.0 Getting Started Guide

    GeneMapper GeneMapper v3.7

    KitPanelMarker Table Settings Auto Bin Bin Set Bin

    Analysis Method

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