IBS Summary File¶

This document describes the structure of the IBS Summary File, a key output used in comparative genomics analyses to record Identical By State (IBS) segments across genomic intervals for a given sample. Along with this summary file, the findIBS command can also produce a BED file format output, which is useful for visualization in genome browsers.

File Format¶

The IBS summary file is a tab-delimited text file where each row represents a genomic region (blocks) for a given sample. Each column is described in detail below.

Column Definitions¶

Column	Data Type	Description
`Block`	`int`	Unique identifier for the genomic block (can be sequential or tool-specific).
`Sample`	`string`	Sample identifier. It is recommended to use standardized identifiers (e.g., `SAM001`, `SAM002`) instead of internal IDs like `LK067`.
`Chromosome`	`string`	Name of the chromosome or scaffold. Standard naming conventions such as `chr1`, `chr2`, ..., `chrUn` (for unplaced scaffolds) should be used.
`Start`	`int`	Start position (0-based, inclusive) of the block in base pairs.
`End`	`int`	End position (0-based, inclusive) of the block in base pairs.
`Length`	`int`	Length of the block in base pairs. Calculated as `End - Start + 1`.
`TotalBlocks`	`int`	Total number of sub-units (or smaller analysis windows) within this block.
`IBSBlocks`	`int`	Number of sub-units within the block that were classified as IBS.
`IBSProportion`	`float`	Fraction of sub-blocks that are IBS. Computed as `IBSBlocks / TotalBlocks`. Ranges from `0.0` to `1.0`.
`MeanScore`	`float`	Mean similarity score across the block (can reflect allele sharing, IBS strength, or other scoring mechanisms depending on the tool used).

Example¶

Block   Sample  Chromosome  Start   End Length  TotalBlocks IBSBlocks   IBSProportion   MeanScore
3495    SAM067  chrUn_01    0   15194   15194   4   4   1.00    0.03
3475    SAM067  chrUn_02    0   59659   59659   12  9   0.75    74.59
3148    SAM067  chr5    1421134 1426134 5000    1   1   1.00    92.11

Note

A high IBSProportion (1.00) indicates that the entire region shows complete similarity across all tested windows.
A low MeanScore may indicate sparse or weak similarity, even if all windows are IBS.
A block with IBSProportion < 1.0 can be indicative of genomic heterogeneity or recombination signals in that region.
Short blocks with high IBS might be less informative than longer blocks with consistent similarity across a large region.