Inversion Report: HsInv0001

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0001

General information

Accession	HsInv0001	Region of the inversion	chr1:2473962-2490316
Status	False	Prediction type	Simple
Estimated Inversion Size	15,184 bp	Supporting predictions	4
Inverted allele frequency	NA	Mechanism of origin	NA
Functional effect	Intergenic breakpoints	Breakpoint 1	chr1:2473962-2475133
Ancestral orientation	NA	Breakpoint 2	chr1:2489145-2490316
Comments	False inversion prediction caused by HG18 assembly error that has been corrected in HG19

- Region map

+ Predictions

- 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

chr1:2473764-2475121

Breakpoint 2

chr1:2489164-2490238

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

chr1:2477117-2477117

Breakpoint 2

chr1:2490251-2490251

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

chr1:2475133-2475133

Breakpoint 2

chr1:2489144-2489144

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

chr1:2456183-2475149

Breakpoint 2

chr1:2489714-2514237

D/C Score

Disc. Support Prob.

Support

121 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	Validated
Genotyping	10 individuals: 8 HapMap/1000GP, 2 Other 10 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.

-Genome Reference Consortium

Description

Update of genome sequence assemblies to correct errors and better represent the existing genome diversity

Method	Genome sequence assembly update
Status	False
Comment	HG18 genome assembly error corrected by the update of the sequence of the same clone (GRC issue HG-21)

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	8	0.0000	1.0000	NA

Africa (AFR)	Africa (AFR) summary	4	8	0.0000	1.0000	NA

+ 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	4	0.0000	1.0000	NA

Europe (EUR)	Europe (EUR) summary	2	4	0.0000	1.0000	NA

+ 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	2	0.0000	1.0000	NA

East Asia (EAS)	East Asia (EAS) summary	2	4	0.0000	1.0000	NA

+ 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

Breakpoint 1	chr1:2473962-2475133	Breakpoint 2	chr1:2489145-2490316
Study	Vicente-Salvador et al. 2017
Description	Breakpoints defined by comparison with the updated HG19 Human Reference assembly, the HuRef Human Genome assembly and four sequenced fosmids
Definition method	Manual curation
Mechanism of origin	NA

Flexibility

9.04

GC content

0.75

Stability

2.43

Comments

HG18 genome assembly error probably caused by inverted SDs 97% identical

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr1:2472669-2475343	2,675	chr1:2488932-2491592	2,661	0.974	Inverted

+ 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	NA	Age	ND
Derived allele	NA	Origin	ND

Breakpoint 1	chr1:2474133-2475149	Breakpoint 2	chr1:2489714-2490144
Assembly	hg18
Definition method	Default informatic definition