Understanding the Columns in Your ChIP-seq Results

The ChIP-seq analysis pipeline generates several result tables, each containing information that can help you interpret your experiment and support downstream analyses. This guide provides a brief description of every downloadable result table and explains the meaning of each column, making it easier to understand the data, identify the metrics most relevant to your analysis, and use the results with confidence.

Note: The examples in this document are based on a Differential Binding Analysis comparing KO and WT sample groups. Therefore, some filenames and column names include these group labels (e.g. Conc_KO, Conc_WT, and KO-WT). In your own analysis, these names will be replaced with the labels of the groups being compared. For example, an analysis comparing Treated and Control samples would contain columns such as Conc_Treated and Conc_Control, and filenames would use Treated-Control instead of KO-WT.

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1. peak_calling_summary.csv

Summary of peak calling results for each sample, including sample metadata and the total number of peaks identified.

Column	Description
sample name	Sample name.
controlName	Name of the control sample used for peak calling (if applicable).
replicate	Biological replicate identifier.
factor	Target protein or histone modification assayed by ChIP-seq.
tissue	Tissue or cell type associated with the sample.
condition	Experimental condition of the sample.
treatment	Treatment applied to the sample, if any.
Peak Count	Total number of peaks identified during the peak calling step.

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2. peak_annotations_stats.csv

This file summarizes the genomic annotation of peaks generated by ChIPseeker.

Column	Description
Feature	Genomic feature assigned to peaks (e.g. Promoter, Exon, Intron, Intergenic).
Frequency	Number of peaks annotated to the corresponding genomic feature.

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3. peak_annotations.csv

This file contains the genomic annotation of every peak generated by ChIPseeker.

• For datasets with biological replicates, the input to ChIPseeker is the IDR output file, which contains only reproducible peaks passing IDR analysis.

• For datasets without biological replicates, the input is the MACS2 narrowPeak file generated during peak calling.

Common genomic annotation columns

These columns are produced by ChIPseeker in both versions of the file:

Column	Description
annotation	Genomic annotation assigned to the peak (e.g. Promoter, Exon, Intron, Intergenic).
geneChr	Chromosome containing the annotated gene.
geneStart	Genomic start coordinate of the annotated gene.
geneEnd	Genomic end coordinate of the annotated gene.
geneLength	Length of the annotated gene in base pairs.
geneStrand	Strand of the annotated gene (+ or −).
geneId	Gene identifier used for annotation.
transcriptId	Transcript identifier associated with the annotation.
distanceToTSS	Distance (bp) from the peak to the nearest transcription start site (TSS). Negative values indicate upstream positions.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GENENAME.x	Gene name from the annotation database.
GENENAME.y	Alternative or additional gene name annotation, when available.

A. Datasets without biological replicates

These columns originate from the MACS2 narrowPeak file:

Column	Description
seqnames	Chromosome containing the peak.
start	Genomic start coordinate of the peak.
end	Genomic end coordinate of the peak.
width	Peak width in base pairs.
strand	Strand information ("." when not applicable).
name	Peak identifier assigned by MACS2.
score	Peak display score (0–1000), proportional to peak strength.
signalValue	Average enrichment signal across the peak.
pValue	Statistical significance of the peak reported as -log10(p-value).
qValue	False discovery rate (FDR) significance reported as -log10(q-value).
peak	Position of the peak summit relative to the peak start (0-based offset).

B. Datasets with biological replicates

These columns originate from the IDR output generated from replicate peak sets:

Column	Description
seqnames	Chromosome containing the reproducible peak.
start	Genomic start coordinate of the reproducible peak.
end	Genomic end coordinate of the reproducible peak.
width	Peak width in base pairs.
strand	Strand information ("." when not applicable).
name_of_region	Identifier assigned to the reproducible peak.
score	IDR score scaled from the reproducibility of the peak (higher scores indicate more reproducible peaks).
signalValue	Enrichment signal of the merged reproducible peak.
pvalue	Statistical significance of the merged peak reported as -log10(p-value).
qvalue	False discovery rate (FDR) significance of the merged peak reported as -log10(q-value).
summit	Genomic position of the merged peak summit.
localIDR	Local IDR score reported as -log10(IDR), measuring reproducibility of the individual peak.
globalIDR	Global IDR score reported as -log10(IDR), measuring reproducibility across all ranked peaks.
rep1_chromStart	Start coordinate of the corresponding peak in replicate 1.
rep1_chromEnd	End coordinate of the corresponding peak in replicate 1.
rep1_signalValue	Enrichment signal of the corresponding peak in replicate 1.
rep1_summit	Summit position of the replicate 1 peak.
rep2_chromStart	Start coordinate of the corresponding peak in replicate 2.
rep2_chromEnd	End coordinate of the corresponding peak in replicate 2.
rep2_signalValue	Enrichment signal of the corresponding peak in replicate 2.
rep2_summit	Summit position of the replicate 2 peak.

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4. pathway_analysis.csv

Results of WikiPathways enrichment analysis performed using clusterProfiler, listing significantly enriched biological pathways.

Column	Description
id	WikiPathways pathway identifier.
description	Name of the enriched pathway.
geneRatio	Proportion of input genes associated with the pathway.
foldEnrichment	Degree of enrichment of the pathway compared to the background gene set.
p.adjust	Multiple testing-adjusted p-value (FDR).
url	Link to the corresponding WikiPathways entry.

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5. gene_ontology_enrichment.csv

Results of Gene Ontology (GO) enrichment analysis performed using clusterProfiler, identifying biological processes, molecular functions, and cellular components enriched in the input gene set.

Column	Description
ONTOLOGY	Gene Ontology category (BP = Biological Process, MF = Molecular Function, CC = Cellular Component).
ID	Gene Ontology (GO) identifier.
Description	Name of the GO term.
GeneRatio	Ratio of input genes associated with the GO term.
GeneRatioN	Number of input genes associated with the GO term.
BgRatio	Ratio of background genes associated with the GO term.
BgRatioN	Number of background genes associated with the GO term.
RichFactor	Ratio of enriched genes to all genes annotated to the GO term.
FoldEnrichment	Degree of enrichment relative to the background gene set.
zScore	Direction and magnitude of enrichment based on observed versus expected genes.
pvalue	Raw enrichment p-value.
p.adjust	Multiple testing-adjusted p-value (FDR).
qvalue	Estimated false discovery rate (q-value).
geneID	List of input genes associated with the GO term.
Count	Number of input genes associated with the GO term.

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6. differential_binding_normalized_counts_annotations.txt

Normalized read counts for all consensus peaks generated by DiffBind, with genomic annotations added using ChIPseeker.

Column	Description
seqnames	Chromosome containing the consensus peak.
start	Genomic start coordinate of the peak.
end	Genomic end coordinate of the peak.
width	Peak width in base pairs.
strand	Strand information ("." when not applicable).
WT_1	Normalized read count for wild-type replicate 1.
WT_2	Normalized read count for wild-type replicate 2.
KO_1	Normalized read count for knockout replicate 1.
KO_2	Normalized read count for knockout replicate 2.
annotation	Genomic annotation assigned to the peak (e.g. Promoter, Exon, Intron, Intergenic).
geneChr	Chromosome containing the annotated gene.
geneStart	Genomic start coordinate of the annotated gene.
geneEnd	Genomic end coordinate of the annotated gene.
geneLength	Length of the annotated gene in base pairs.
geneStrand	Strand of the annotated gene (+ or −).
geneId	Gene identifier used for annotation.
transcriptId	Transcript identifier associated with the annotation.
distanceToTSS	Distance (bp) from the peak to the nearest transcription start site (TSS). Negative values indicate upstream positions.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Full description of the annotated gene.

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7. binding_affinity_top_1000_peaks.txt

The top 1,000 differentially bound peaks ranked by statistical significance, used to generate the Binding Affinity plot. The file includes differential binding statistics, normalized read counts, and ChIPseeker peak annotations.

Column	Description
seqnames	Chromosome containing the peak.
start	Genomic start coordinate of the peak.
end	Genomic end coordinate of the peak.
width	Peak width in base pairs.
strand	Strand information ("." when not applicable).
Conc	Mean normalized binding affinity across all samples.
Conc_KO	Mean normalized binding affinity in the KO group.
Conc_WT	Mean normalized binding affinity in the WT group.
Fold	Log2 fold change in binding affinity between the two experimental groups. Positive values indicate higher binding in the first group of the comparison.
p.value	Raw p-value for differential binding.
FDR	False discovery rate (adjusted p-value).
KO_1	Normalized read count for knockout replicate 1.
KO_2	Normalized read count for knockout replicate 2.
WT_1	Normalized read count for wild-type replicate 1.
WT_2	Normalized read count for wild-type replicate 2.
annotation	Genomic annotation assigned to the peak (e.g. Promoter, Exon, Intron, Intergenic).
geneChr	Chromosome containing the annotated gene.
geneStart	Genomic start coordinate of the annotated gene.
geneEnd	Genomic end coordinate of the annotated gene.
geneLength	Length of the annotated gene in base pairs.
geneStrand	Strand of the annotated gene (+ or −).
geneId	Gene identifier used for annotation.
transcriptId	Transcript identifier associated with the annotation.
distanceToTSS	Distance (bp) from the peak to the nearest transcription start site (TSS). Negative values indicate upstream positions.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Full description of the annotated gene.

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8. KO-WT_differential_binding_results_annotations.txt

Complete differential binding analysis results generated by DiffBind, including differential binding statistics, normalized read counts, and genomic annotations produced by ChIPseeker.

Column	Description
seqnames	Chromosome containing the peak.
start	Genomic start coordinate of the peak.
end	Genomic end coordinate of the peak.
width	Peak width in base pairs.
strand	Strand information ("." when not applicable).
Conc	Mean normalized binding affinity across all samples.
Conc_KO	Mean normalized binding affinity in the KO group.
Conc_WT	Mean normalized binding affinity in the WT group.
Fold	Log2 fold change in binding affinity between the two experimental groups. Positive values indicate higher binding in the first group of the comparison.
p.value	Raw p-value for differential binding.
FDR	False discovery rate (adjusted p-value).
KO_1	Normalized read count for knockout replicate 1.
KO_2	Normalized read count for knockout replicate 2.
WT_1	Normalized read count for wild-type replicate 1.
WT_2	Normalized read count for wild-type replicate 2.
annotation	Genomic annotation assigned to the peak (e.g. Promoter, Exon, Intron, Intergenic).
geneChr	Chromosome containing the annotated gene.
geneStart	Genomic start coordinate of the annotated gene.
geneEnd	Genomic end coordinate of the annotated gene.
geneLength	Length of the annotated gene in base pairs.
geneStrand	Strand of the annotated gene (+ or −).
geneId	Gene identifier used for annotation.
transcriptId	Transcript identifier associated with the annotation.
distanceToTSS	Distance (bp) from the peak to the nearest transcription start site (TSS). Negative values indicate upstream positions.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Full description of the annotated gene.

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9. DBA_results_contrasts_summary.txt

Summary of the Differential Binding Analysis contrasts, showing the sample groups compared and the number of significantly differentially bound peaks identified by each statistical method.

Column	Description
Factor	Experimental factor used to define the comparison (e.g. treatment or genotype).
Group	Name of the first sample group in the comparison.
Samples	Number of samples included in the first group.
Group2	Name of the second sample group in the comparison.
Samples2	Number of samples included in the second group.
DB.edgeR	Number of significantly differentially bound peaks identified by the edgeR method.
DB.DESeq2	Number of significantly differentially bound peaks identified by the DESeq2 method.

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10. 1f_KO-WT_DBA_results_peak_annotation_stats.txt

Summary of the genomic features assigned to differentially bound peaks for the KO vs WT comparison generated by ChIPseeker, showing the number of peaks annotated to each feature type.

Column	Description
Feature	Genomic feature assigned to the peak (e.g. Promoter, Exon, Intron, Intergenic).
Frequency	Number of differentially bound peaks assigned to the corresponding feature.

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11. 1f_KO-WT_DBA_annotated_peaks.txt

Differentially bound peaks identified by DiffBind for the KO vs WT comparison, annotated with nearby genes and genomic features using ChIPseeker.

Column	Description
seqnames	Chromosome containing the peak.
start	Genomic start position of the peak.
end	Genomic end position of the peak.
width	Length of the peak in base pairs.
strand	Genomic strand of the annotated feature, when applicable.
Conc	Average normalized binding affinity across all samples.
Conc_KO	Average normalized binding affinity in the KO group.
Conc_WT	Average normalized binding affinity in the WT group.
Fold	Log2 fold change in binding between KO and WT.
p.value	Statistical significance of differential binding.
FDR	False discovery rate (multiple testing adjusted p-value).
annotation	Genomic annotation assigned to the peak (e.g. Promoter, Intron, Intergenic).
geneChr	Chromosome of the annotated gene.
geneStart	Genomic start position of the annotated gene.
geneEnd	Genomic end position of the annotated gene.
geneLength	Length of the annotated gene in base pairs.
geneStrand	Strand of the annotated gene.
geneId	Gene identifier associated with the annotated peak.
transcriptId	Transcript identifier associated with the annotated peak.
distanceToTSS	Distance from the peak to the transcription start site (TSS).
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Description of the annotated gene.

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12. 1f_KO-WT_edgeR_DBA_significant_peaks.txt

Differentially bound peaks identified as significant by the edgeR analysis for the KO vs WT comparison, with associated gene annotations.

Column	Description
Chr	Chromosome containing the peak.
Start	Genomic start position of the peak.
End	Genomic end position of the peak.
Score	Peak score from the original peak set.
Conc	Average normalized binding affinity across all samples.
Conc_KO	Average normalized binding affinity in the KO group.
Conc_WT	Average normalized binding affinity in the WT group.
Fold	Log2 fold change in binding between KO and WT.
p-value	Statistical significance of differential binding.
FDR	False discovery rate (multiple testing adjusted p-value).
Chr_Start	Combined chromosome and start coordinate used as a unique peak identifier.
geneId	Gene identifier associated with the peak.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Description of the annotated gene.

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13. 1f_KO-WT_DESeq2_DBA_significant_peaks.txt

Differentially bound peaks identified as significant by the DESeq2 analysis for the KO vs WT comparison, with associated gene annotations.

Column	Description
Chr	Chromosome containing the peak.
Start	Genomic start position of the peak.
End	Genomic end position of the peak.
Score	Peak score from the original peak set.
Conc	Average normalized binding affinity across all samples.
Conc_KO	Average normalized binding affinity in the KO group.
Conc_WT	Average normalized binding affinity in the WT group.
Fold	Log2 fold change in binding between KO and WT.
p-value	Statistical significance of differential binding.
FDR	False discovery rate (multiple testing adjusted p-value).
Chr_Start	Combined chromosome and start coordinate used as a unique peak identifier.
geneId	Gene identifier associated with the peak.
ENSEMBL	Ensembl gene identifier.
SYMBOL	Official gene symbol.
GeneDescription	Description of the annotated gene.

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