Inversion Report: HsInv0066

+ 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

chr8:6139497-6139497

Breakpoint 2

chr8:6145843-6145843

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

chr8:6137097-6142045

Breakpoint 2

chr8:6145165-6153909

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

chr8:6141963-6142677

Breakpoint 2

chr8:6144803-6145505

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

chr8:6140460-6140460

Breakpoint 2

chr8:6143822-6143822

Individuals

NA15510	NA18505

Name

Breakpoint 1

chr8:6141586-6141586

Breakpoint 2

chr8:6142940-6142940

Individuals

NA15510	NA18505

Name

Breakpoint 1

chr8:6144689-6144689

Breakpoint 2

chr8:6146629-6146629

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

chr8:6142791-6142791

Breakpoint 2

chr8:6144697-6144697

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

chr8:6107683-6142380

Breakpoint 2

chr8:6145194-6177984

D/C Score

0.33

Disc. Support Prob.

0.99839

Support

12 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

+ Validation and genotyping

-Vicente-Salvador et al. 2017

Description

Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes

Method	Polymerase chain reaction (PCR)
Status	False

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.

-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 CH17-9E4 BAC sequence (AC255547) 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:

-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:

+ Frequency

+ Breakpoints

Breakpoint 1	chr8:6141791-6142380	Breakpoint 2	chr8:6145194-6145697
Definition method	Default informatic definition
Mechanism of origin	NA

Flexibility

10.49

GC content

0.47

Stability

1.9

Sequence features
Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr8:6141654-6142791	1,138	chr8:6144698-6145833	1,136	0.979	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Ancestral allele	NA	Age	ND
Derived allele	NA	Origin	ND

Accession	HsInv0066	Region of the inversion	chr8:6141791-6145697
Status	False	Prediction type	Simple
Estimated Inversion Size	3,361 bp	Supporting predictions	8
Inverted allele frequency	NA	Mechanism of origin	NA
Functional effect	Intergenic breakpoints	Breakpoint 1	chr8:6141791-6142380
Ancestral orientation	NA	Breakpoint 2	chr8:6145194-6145697