Resource
| Id | ATAC-seq/ENCSR355SGJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR355SGJ [biosample_summary="Homo sapiens sigmoid 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 {ENCAN021SBP|/analyses/ENCAN021SBP/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN021SBP|/analyses/ENCAN021SBP/} has in progress subobject document {01d536a1-9747-4f99-9af4-f310dcea5457|/documents/01d536a1-9747-4f99-9af4-f310dcea5457/} 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. {ENCFF846PJS|/files/ENCFF846PJS/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. 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 {ENCFF205MPN|/files/ENCFF205MPN/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.848789. 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 {ENCFF205MPN|/files/ENCFF205MPN/} 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_ENCSR355SGJ | float |
ATAC-seq_ENCSR355SGJ |
ATAC-seq ENCSR355SGJ [biosample_summary="Homo sapiens sigmoid colon tissue female adult (51 years)"]
|
 |
[1.5, 26.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42887741 | 1.33% | 71989 |
| chr1 | 4213952 | 1.69% | 6910 |
| chr2 | 3415816 | 1.41% | 5865 |
| chr3 | 2674560 | 1.35% | 4641 |
| chr4 | 1917863 | 1.01% | 3412 |
| chr5 | 2206847 | 1.22% | 3788 |
| chr6 | 2446491 | 1.43% | 4162 |
| chr7 | 2219355 | 1.39% | 3799 |
| chr8 | 1867560 | 1.29% | 3277 |
| chr9 | 1935075 | 1.40% | 3269 |
| chr10 | 2174911 | 1.63% | 3738 |
| chr11 | 2234128 | 1.65% | 3630 |
| chr12 | 2127519 | 1.60% | 3553 |
| chr13 | 987138 | 0.86% | 1738 |
| chr14 | 1392936 | 1.30% | 2338 |
| chr15 | 1442560 | 1.41% | 2378 |
| chr16 | 1510901 | 1.67% | 2381 |
| chr17 | 2036005 | 2.45% | 3189 |
| chr18 | 871427 | 1.08% | 1553 |
| chr19 | 1693990 | 2.89% | 2533 |
| chr20 | 1093985 | 1.70% | 1822 |
| chr21 | 514551 | 1.10% | 874 |
| chr22 | 858554 | 1.69% | 1387 |
| chrX | 1050354 | 0.67% | 1747 |
| chrY | 1263 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 71989 | 150 | 3025 | 595.75 | 479 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF846PJS.bed.gz | 3.25 MB | 49e58c563079fb74c04ff5d64e55d976 |
| ENCFF846PJS.tabix.bed.gz | 826.06 KB | 7956a90ff14879f37b376bf506610b7c |
| ENCFF846PJS.tabix.bed.gz.tbi | 354.75 KB | 008a99b5dd936fb19463a1d12d9710e3 |
| genomic_resource.yaml | 3.2 KB | 9d7711bbcf3ffaacc6a7d7985ddd3b9a |
| statistics/ |