Resource
| Id | ATAC-seq/ENCSR386HAZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR386HAZ [biosample_summary="Homo sapiens transverse colon tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN571WPB|/analyses/ENCAN571WPB/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN571WPB|/analyses/ENCAN571WPB/} has in progress subobject document {d0d3b944-6c96-48db-8cb4-30011c65929d|/documents/d0d3b944-6c96-48db-8cb4-30011c65929d/} audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF355GMG|/files/ENCFF355GMG/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.15. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF422XWI|/files/ENCFF422XWI/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.848744. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF422XWI|/files/ENCFF422XWI/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR386HAZ | float |
ATAC-seq_ENCSR386HAZ |
ATAC-seq ENCSR386HAZ [biosample_summary="Homo sapiens transverse colon tissue female adult (51 years)"]
|
 |
[1.48, 28.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 49496974 | 1.54% | 90599 |
| chr1 | 4776127 | 1.92% | 8557 |
| chr2 | 4131333 | 1.71% | 7755 |
| chr3 | 3153038 | 1.59% | 5897 |
| chr4 | 2435878 | 1.28% | 4577 |
| chr5 | 2641036 | 1.45% | 4993 |
| chr6 | 2907818 | 1.70% | 5404 |
| chr7 | 2669709 | 1.68% | 4981 |
| chr8 | 2202303 | 1.52% | 4155 |
| chr9 | 2207998 | 1.60% | 4044 |
| chr10 | 2424140 | 1.81% | 4581 |
| chr11 | 2630467 | 1.95% | 4742 |
| chr12 | 2409781 | 1.81% | 4365 |
| chr13 | 1191750 | 1.04% | 2240 |
| chr14 | 1549328 | 1.45% | 2799 |
| chr15 | 1548637 | 1.52% | 2833 |
| chr16 | 1720417 | 1.90% | 3031 |
| chr17 | 2173397 | 2.61% | 3761 |
| chr18 | 1030607 | 1.28% | 1973 |
| chr19 | 1780680 | 3.04% | 2877 |
| chr20 | 1215899 | 1.89% | 2199 |
| chr21 | 590068 | 1.26% | 1103 |
| chr22 | 849809 | 1.67% | 1513 |
| chrX | 1255466 | 0.80% | 2214 |
| chrY | 1288 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 90599 | 150 | 3127 | 546.33 | 439 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF355GMG.bed.gz | 3.77 MB | d61e3f1a4aba9927abcda5fd53ba9211 |
| ENCFF355GMG.tabix.bed.gz | 1.01 MB | c9b903a7b7421c8bba37e2f0bac0144e |
| ENCFF355GMG.tabix.bed.gz.tbi | 407.73 KB | 6cb5d7878c201ed8d99011a617c98f29 |
| genomic_resource.yaml | 3.21 KB | 90d8e5703c07259ec68fd8a91df37574 |
| statistics/ |