Interpreting CRISPR outputs
Guide RNA tables, on-target scores, off-target site reports, and CRISPR screen gene rankings.
crisproutputs
These tools return ranked guide RNA tables with on-target scores, off-target site reports with mismatch counts, and screen gene rankings — letting you pick a high-efficiency, low-risk guide for the bench or shortlist screen hits for follow-up.
Interpreting CRISPR outputs
Guide RNA Design output
| Field | Type | Description |
|---|---|---|
gene | string | Target gene symbol |
organism | string | Target organism |
pam | string | PAM sequence used |
total_sites | number | Total PAM sites found in the target region |
returned_count | number | Number of guides returned (after filtering) |
guides | array | Ranked guide RNA candidates |
Guide fields
| Field | Type | Description |
|---|---|---|
rank | number | Rank by on-target score (1 = best) |
sequence | string | 20-nt guide RNA sequence (DNA) |
pam_sequence | string | PAM sequence at the target site |
strand | string | Target strand (+ or -) |
chromosome | string | Chromosome name |
position | number | Genomic start position |
exon | string | Exon name if in a coding exon (e.g., exon3) |
gc_content | number | GC percentage of the guide (0-100) |
on_target_score | number | Predicted cutting efficiency (0-1) |
On-target score interpretation
| Score Range | Interpretation |
|---|---|
| 0.7 - 1.0 | High predicted activity; recommended |
| 0.5 - 0.7 | Moderate activity; acceptable for most experiments |
| 0.3 - 0.5 | Low activity; may require higher MOI or alternative delivery |
| < 0.3 | Poor predicted activity; not recommended |
GC content guidelines
| GC% | Interpretation |
|---|---|
| 40 - 60% | Optimal range for most applications |
| 30 - 40% or 60 - 70% | Acceptable; may have slightly reduced activity |
| < 30% or > 70% | Suboptimal; higher risk of secondary structure or stability issues |
Off-Target Analysis output
| Field | Type | Description |
|---|---|---|
guide | string | Query guide sequence |
genome | string | Reference genome used |
pam | string | PAM filter applied |
total_offtargets | number | Total off-target sites found |
offtargets_by_mismatch | object | Count of sites per mismatch level |
sites | array | Off-target site details |
Off-target site fields
| Field | Type | Description |
|---|---|---|
sequence | string | Off-target genomic sequence |
mismatches | number | Number of mismatches relative to the guide |
mismatch_positions | number[] | Positions where mismatches occur (1-indexed from PAM-proximal end) |
chromosome | string | Chromosome |
position | number | Genomic position |
strand | string | Strand (+ or -) |
gene | string | Nearest gene symbol (or -- if intergenic) |
in_cds | boolean | Whether the site falls within a coding sequence |
in_exon | boolean | Whether the site falls within any exon |
Off-target risk assessment
| Mismatch Count | 0 | 1 | 2 | 3 |
|---|---|---|---|---|
| Expected | 1 (on-target) | 0-2 | 0-20 | 0-200 |
| Concern level | N/A | High | Moderate | Low |
A guide is considered low-risk when:
- Zero 1-mismatch off-target sites outside the intended target
- Fewer than 5 sites at 2 mismatches in coding regions
- No off-target sites in known essential genes
Screen Analysis output
| Field | Type | Description |
|---|---|---|
analysis_type | string | "mageck" |
direction | string | Analysis direction (negative, positive, or both) |
total_genes | number | Total genes analyzed |
significant_genes | number | Genes passing FDR threshold |
fdr_threshold | number | FDR cutoff used |
gene_rankings | array | Gene-level results sorted by significance |
Gene ranking fields
| Field | Type | Description |
|---|---|---|
rank | number | Gene rank (1 = most significant) |
gene | string | Gene symbol |
num_guides | number | Number of guides targeting this gene |
guides_significant | number | Guides showing consistent effect |
rra_score | number | Robust Rank Aggregation score (lower = more significant) |
p_value | number | Gene-level p-value |
fdr | number | Benjamini-Hochberg adjusted p-value |
lfc | number | Median log2 fold change across guides |
significant | boolean | Whether the gene passes FDR threshold |
RRA score interpretation
| RRA Score | Interpretation |
|---|---|
| < 1e-5 | Very strong hit; high confidence |
| 1e-5 to 1e-3 | Strong hit; likely true positive |
| 1e-3 to 0.01 | Moderate hit; requires validation |
| > 0.01 | Weak or non-significant |
Log2 fold change interpretation
| Direction | LFC < 0 | LFC > 0 |
|---|---|---|
| Negative selection | Guide depletion (essential gene) | Guide enrichment (not depleted) |
| Positive selection | Guide depletion (not enriched) | Guide enrichment (resistance gene) |
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Gene targets, PAM types, scoring models, mismatch thresholds, and screen analysis options for all CRISPR tools.
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