Inversion Report: HsInv0064

+ Predictions

- Chaisson et al. 2015

Description	Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1)
Method	Long-read sequencing

Name

Breakpoint 1

chr7:106845711-106845711

Breakpoint 2

chr7:106850968-106850968

Individuals

CHM1

- Pang et al. 2010

Description	Paired-end mapping analysis of the J. Craig Venter genome (HuRef)
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr7:106840221-106846108

Breakpoint 2

chr7:106850529-106855308

Individuals

HuRef

- McKernan et al. 2009

Description	Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr7:106845746-106846657

Breakpoint 2

chr7:106850909-106850922

Individuals

NA18507

- Korbel et al. 2007

Description	Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr7:106845405-106845405

Breakpoint 2

chr7:106846837-106846837

Individuals

NA15510	NA18505

Name

Breakpoint 1

chr7:106848172-106848172

Breakpoint 2

chr7:106850981-106850981

Individuals

NA15510	NA18505

Name

Breakpoint 1

chr7:106848177-106848177

Breakpoint 2

chr7:106850951-106850951

Individuals

NA15510	NA18505

- Levy et al. 2007

Description	Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef)
Method	Genome sequence comparison

Name

Breakpoint 1

chr7:106846308-106846308

Breakpoint 2

chr7:106850371-106850371

Individuals

HuRef

- Martinez-Fundichely et al. 2014 (in preparation)

Description	Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr7:106813650-106846862

Breakpoint 2

chr7:106850773-106884944

D/C Score

NA

Disc. Support Prob.

0.99025

Support

13 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

+ Validation and genotyping

-Chaisson et al. 2015

Description

Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1)

Method	Sequence analysis
Status	Validated
Comment	Inversion validated by analysis of CH17-150B4 BAC sequence (AC255406) obtained with PacBio long reads

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

Only modified sections are submitted. All the corresponding fields must be complete because they will be overwritten. In the Frequency without genotypes section multiple populations can be added if the editing process is repeated for each one of them.

-Korbel et al. 2007

Description

Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly

Method	Polymerase chain reaction (PCR)
Status	Validated

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

Method	Genome sequence comparison
Status	Validated
Comment	Inversion confirmed by comparison with the Celera Human Genome assembly

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

+ Frequency

+ Breakpoints

+ Evolutionary history

+ Functional effects

+ Report history

Accession	HsInv0064	Region of the inversion	chr7:106845308-106851371
Status	Validated	Prediction type	Simple
Estimated Inversion Size	4,988 bp	Supporting predictions	8
Inverted allele frequency	ND	Mechanism of origin	NAHR
Functional effect	Inverts a region within an intron of a gene	Breakpoint 1	chr7:106845308-106846862
Ancestral orientation	NA	Breakpoint 2	chr7:106850773-106851371
Comments	Standard orientation is possibly a low frequency variant or HG18 assembly error

Breakpoint 1	chr7:106845308-106846862	Breakpoint 2	chr7:106850773-106851371
Definition method	Default informatic definition
Mechanism of origin	NAHR

Ancestral allele	NA	Age	ND
Derived allele	NA	Origin	ND

Gene position	chr7:106635533-106992195
Mechanism	Inverts a region within an intron of a gene

Breakpoint 1	chr7:106845308-106846862	Breakpoint 2	chr7:106850773-106851371
Assembly	hg18
Definition method	Default informatic definition