Inversion Report: HsInv0015

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0015

General information

Accession	HsInv0015	Region of the inversion	chr10:13144983-13145283
Status	Validated	Prediction type	Simple
Estimated Inversion Size	269 bp	Supporting predictions	5
Inverted allele frequency	0.8500	Mechanism of origin	FoSTeS
Functional effect	Intergenic breakpoints	Breakpoint 1	chr10:13144983-13145043
Ancestral orientation	Standard	Breakpoint 2	chr10:13145279-13145283
Comments	Derived allele includes a 61-bp duplication, a 5-bp deletion and a 14-bp insertion from Chr. 3 flanking the inverted region

- Region map

+ Predictions

- Sudmant et al. 2015

Description	Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data
Method	Paired-end mapping (PEM), Long-read sequencing

Name
Breakpoint 1	chr10:13144908-13144908	Breakpoint 2	chr10:13145303-13145303
Individuals	2266 out of 2504 individuals

- 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

chr10:13144093-13145001

Breakpoint 2

chr10:13145280-13146242

Individuals

NA18507

- Ahn et al. 2009

Description	Next generation sequencing and analysis by paired-end mapping of a Korean individual genome
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr10:13144875-13145138

Breakpoint 2

chr10:13145123-13145522

Individuals

SJK

- Wang et al. 2008

Description	Next-generation sequencing and analysis by paired-end mapping of a male Han Chinese individual genome
Method	Paired-end mapping (PEM)

Name
Breakpoint 1	chr10:13145005-13145005	Breakpoint 2	chr10:13145287-13145287
Individuals

- 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

chr10:13145105-13145105

Breakpoint 2

chr10:13145278-13145278

Individuals

HuRef

+ 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	Validated
Genotyping	10 individuals: 8 HapMap/1000GP, 2 Other 3 STD/INV - 7 INV/INV

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.

-Sudmant et al. 2015

Description

Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data

Method	Sequence analysis
Status	Validated
Comment	Simple inversion validated by sequence analysis of PacBio long reads from fosmids, PacBio long reads from CHM1 genome

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

- Frequency

+ Africa (AFR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Yoruba	Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017)	4	7	0.1250	0.8750	> 0.5

Africa (AFR)	Africa (AFR) summary	4	7	0.1250	0.8750	> 0.5

+ Europe (EUR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Northwestern European	Utah residents with Northern and Western European ancestry (CEU) (Vicente-Salvador et al. 2017)	2	3	0.2500	0.7500	> 0.5

Europe (EUR)	Europe (EUR) summary	2	3	0.2500	0.7500	> 0.5

+ East Asia (EAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Han Chinese	Han Chinese in Beijing, China (CHB) (Vicente-Salvador et al. 2017)	1	2	0.0000	1.0000	NA
Japanese	Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017)	1	1	0.5000	0.5000	> 0.3

East Asia (EAS)	East Asia (EAS) summary	2	3	0.2500	0.7500	> 0.5

+ Unknown

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Unknown	Unknown (Vicente-Salvador et al. 2017)	2	4	0.0000	1.0000	NA

Unknown	Unknown summary	2	4	0.0000	1.0000	NA

+ Breakpoints

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona

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

Ancestral allele	Standard	Age	ND
Derived allele	Inverted	Origin	ND

Breakpoint 1	chr10:13144538-13145475	Breakpoint 2	chr10:13144922-13145723
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr10:13144538-13145475	Breakpoint 2	chr10:13144922-13145723
Assembly	hg18
Definition method	Default informatic definition

Species	Orientation	Method	Study
Chimpanzee	Standard	Polymerase chain reaction (PCR)	Vicente-Salvador et al. 2017
Gorilla	Standard	Polymerase chain reaction (PCR)	Vicente-Salvador et al. 2017
Rhesus macaque	Standard	Genome sequence comparison	Vicente-Salvador et al. 2017