Inversion Report: HsInv0074

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0074

General information

Accession	HsInv0074	Region of the inversion	chrX:48899567-48907237
Status	Validated	Prediction type	Simple
Estimated Inversion Size	6,350 bp	Supporting predictions	6
Inverted allele frequency	ND	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chrX:48899567-48901053
Ancestral orientation	NA	Breakpoint 2	chrX:48906080-48907237
Comments	Standard orientation is possibly a low frequency variant or HG18 assembly error

- Region map

+ 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

chrX:48899128-48899128

Breakpoint 2

chrX:48907656-48907656

Individuals

CHM1

- 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

chrX:48900054-48900518

Breakpoint 2

chrX:48906269-48906706

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

chrX:48901626-48901626

Breakpoint 2

chrX:48907753-48907753

Individuals

NA15510	NA18505

Name

Breakpoint 1

chrX:48903902-48903902

Breakpoint 2

chrX:48907320-48907320

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

chrX:48900567-48900567

Breakpoint 2

chrX:48906237-48906237

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

chrX:48869280-48901053

Breakpoint 2

chrX:48906080-48937895

D/C Score

Disc. Support Prob.

Support

33 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

+ Validation and genotyping

-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	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:

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.

Method	Polymerase chain reaction (PCR)
Status	Validated

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

+ Frequency

+ Breakpoints

Breakpoint 1	chrX:48899567-48901053	Breakpoint 2	chrX:48906080-48907237
Definition method	Default informatic definition
Mechanism of origin	NAHR

Flexibility

9.72

GC content

0.71

Stability

2.32

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between 1.6 kb inverted SDs with 93% identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chrX:48899128-48900724	1,597	chrX:48906081-48907656	1,576	0.934	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Hospital del Mar Research Institute

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Ancestral allele	NA	Age	ND
Derived allele	NA	Origin	ND