Resource
| Id | ATAC-seq/ENCSR587TRP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR587TRP [biosample_summary="Homo sapiens SK-N-SH treated with 6 \u03BC\ M all-trans-retinoic acid for 48 hours"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: treated with 6 μM all-trans-retinoic acid for 48 hours output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN752KCW|/analyses/ENCAN752KCW/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN752KCW|/analyses/ENCAN752KCW/} has in progress subobject document {4b73c5ee-3525-4422-85bb-2df42d4f53a6|/documents/4b73c5ee-3525-4422-85bb-2df42d4f53a6/} 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 {ENCFF049RWL|/files/ENCFF049RWL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.874478. 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 {ENCFF049RWL|/files/ENCFF049RWL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. 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 {ENCFF270AGJ|/files/ENCFF270AGJ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.874897. 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 {ENCFF270AGJ|/files/ENCFF270AGJ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. 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 {ENCFF502IYP|/files/ENCFF502IYP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.870587. 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 {ENCFF502IYP|/files/ENCFF502IYP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR587TRP | float |
ATAC-seq_ENCSR587TRP |
ATAC-seq ENCSR587TRP [biosample_summary="Homo sapiens SK-N-SH treated with 6 \u03BC\ M all-trans-retinoic acid for 48 hours"]
|
 |
[1.26, 40.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 105908862 | 3.29% | 146096 |
| chr1 | 11314353 | 4.54% | 15342 |
| chr2 | 8824644 | 3.64% | 12311 |
| chr3 | 6959939 | 3.51% | 9783 |
| chr4 | 5415447 | 2.85% | 7828 |
| chr5 | 5936360 | 3.27% | 8346 |
| chr6 | 6177487 | 3.62% | 8630 |
| chr7 | 6690691 | 4.20% | 9169 |
| chr8 | 4440165 | 3.06% | 6235 |
| chr9 | 4441513 | 3.21% | 6043 |
| chr10 | 4877617 | 3.65% | 6719 |
| chr11 | 5210856 | 3.86% | 7080 |
| chr12 | 5066578 | 3.80% | 6995 |
| chr13 | 2931398 | 2.56% | 4229 |
| chr14 | 3018776 | 2.82% | 4134 |
| chr15 | 3352251 | 3.29% | 4620 |
| chr16 | 3165441 | 3.50% | 4144 |
| chr17 | 4708250 | 5.66% | 6150 |
| chr18 | 2147753 | 2.67% | 3103 |
| chr19 | 3180740 | 5.43% | 4089 |
| chr20 | 2411230 | 3.74% | 3353 |
| chr21 | 1099846 | 2.35% | 1494 |
| chr22 | 1709087 | 3.36% | 2299 |
| chrX | 2827724 | 1.81% | 3997 |
| chrY | 716 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 146096 | 150 | 3731 | 724.93 | 624 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF716JUM.bed.gz | 6.82 MB | a94091f4d35bdcbb5ce551fad645f0fd |
| ENCFF716JUM.tabix.bed.gz | 1.64 MB | bec81a3975e73483077ba9d0ad7df2c6 |
| ENCFF716JUM.tabix.bed.gz.tbi | 491.12 KB | 197d46ca5516b1622c4d4c55a058e6ff |
| genomic_resource.yaml | 5.43 KB | a7c4dd4bb94ed0cd4441001885a80908 |
| statistics/ |