Resource
| Id | ATAC-seq/ENCSR165FYY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR165FYY [biosample_summary="Homo sapiens central memory CD8-positive, alpha-beta T cell male adult (36 years)"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (36 years) output_type: replicated peaks audit_error: Alignment file {ENCFF613OUT|/files/ENCFF613OUT/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 4927242 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_error: Alignment file {ENCFF485AVO|/files/ENCFF485AVO/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 10716289 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_internal_action: Released analysis {ENCAN728UUJ|/analyses/ENCAN728UUJ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: 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 {ENCFF613OUT|/files/ENCFF613OUT/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.133673. audit_not_compliant: 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 {ENCFF613OUT|/files/ENCFF613OUT/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.08. audit_not_compliant: 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 {ENCFF485AVO|/files/ENCFF485AVO/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.265203. audit_not_compliant: 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 {ENCFF485AVO|/files/ENCFF485AVO/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.18. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed file {ENCFF613OUT|/files/ENCFF613OUT/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.27. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed file {ENCFF485AVO|/files/ENCFF485AVO/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.01. audit_warning: 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. {ENCFF751LGG|/files/ENCFF751LGG/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.48. audit_warning: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF662SIF|/files/ENCFF662SIF/} (overlap peaks) and {ENCFF270DPY|/files/ENCFF270DPY/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 94804 and 63083 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR165FYY | float |
ATAC-seq_ENCSR165FYY |
ATAC-seq ENCSR165FYY [biosample_summary="Homo sapiens central memory CD8-positive, alpha-beta T cell male adult (36 years)"]
|
 |
[1.46, 40.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 31818060 | 0.99% | 56203 |
| chr1 | 3212859 | 1.29% | 5578 |
| chr2 | 2393592 | 0.99% | 4342 |
| chr3 | 1861593 | 0.94% | 3339 |
| chr4 | 1186234 | 0.62% | 2122 |
| chr5 | 1511939 | 0.83% | 2669 |
| chr6 | 1950414 | 1.14% | 3442 |
| chr7 | 1591860 | 1.00% | 2870 |
| chr8 | 1207588 | 0.83% | 2192 |
| chr9 | 1227990 | 0.89% | 2176 |
| chr10 | 1465378 | 1.10% | 2612 |
| chr11 | 1580501 | 1.17% | 2757 |
| chr12 | 1618108 | 1.21% | 2848 |
| chr13 | 714434 | 0.62% | 1278 |
| chr14 | 1094992 | 1.02% | 1957 |
| chr15 | 1030345 | 1.01% | 1825 |
| chr16 | 1257939 | 1.39% | 2159 |
| chr17 | 1728513 | 2.08% | 2969 |
| chr18 | 567961 | 0.71% | 1062 |
| chr19 | 1622992 | 2.77% | 2738 |
| chr20 | 852804 | 1.32% | 1534 |
| chr21 | 400721 | 0.86% | 705 |
| chr22 | 731470 | 1.44% | 1266 |
| chrX | 905293 | 0.58% | 1563 |
| chrY | 102540 | 0.18% | 200 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56203 | 150 | 2487 | 566.13 | 462 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF662SIF.bed.gz | 2.27 MB | ae65f4555dfc9ed09c5e5ce6fd745e75 |
| ENCFF662SIF.tabix.bed.gz | 636.84 KB | 74e70537136fa7e7dcdc607e08cd85d6 |
| ENCFF662SIF.tabix.bed.gz.tbi | 275.01 KB | 4c51732590fe85ba63240a5904e65aff |
| genomic_resource.yaml | 6.93 KB | 234ea8ca7d71e90a7fc88559d1cb8c60 |
| statistics/ |