Resource
| Id | ATAC-seq/ENCSR032MEH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR032MEH [biosample_summary="Homo sapiens T-cell male adult (43 years)"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (43 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN854QMS|/analyses/ENCAN854QMS/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: Transcription Start Site (TSS) enrichment values for alignments to the human genome GRCh38 are concerning when < 5, acceptable between 5 and 7, and ideal when > 7. ENCODE processed file {ENCFF400ZNW|/files/ENCFF400ZNW/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a TSS enrichment value of 1.9192740289086339. audit_not_compliant: Transcription Start Site (TSS) enrichment values for alignments to the human genome GRCh38 are concerning when < 5, acceptable between 5 and 7, and ideal when > 7. ENCODE processed file {ENCFF410WTM|/files/ENCFF410WTM/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a TSS enrichment value of 2.010155365758926. 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. {ENCFF105ZAX|/files/ENCFF105ZAX/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.05. 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 {ENCFF410WTM|/files/ENCFF410WTM/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.794959. 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 {ENCFF410WTM|/files/ENCFF410WTM/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.79. 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) {ENCFF105ZAX|/files/ENCFF105ZAX/} (overlap peaks) and {ENCFF206PEF|/files/ENCFF206PEF/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 105476 and 1703 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR032MEH | float |
ATAC-seq_ENCSR032MEH |
ATAC-seq ENCSR032MEH [biosample_summary="Homo sapiens T-cell male adult (43 years)"]
|
 |
[1.38, 29.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33292976 | 1.03% | 70129 |
| chr1 | 3098719 | 1.24% | 6656 |
| chr2 | 2332965 | 0.96% | 4994 |
| chr3 | 1374037 | 0.69% | 3030 |
| chr4 | 1040318 | 0.55% | 2161 |
| chr5 | 1386120 | 0.76% | 2899 |
| chr6 | 1373874 | 0.80% | 2953 |
| chr7 | 1864036 | 1.17% | 3901 |
| chr8 | 1194224 | 0.82% | 2514 |
| chr9 | 1568726 | 1.13% | 3246 |
| chr10 | 1718103 | 1.28% | 3647 |
| chr11 | 1621229 | 1.20% | 3423 |
| chr12 | 1320291 | 0.99% | 2874 |
| chr13 | 684960 | 0.60% | 1395 |
| chr14 | 1077004 | 1.01% | 2235 |
| chr15 | 1282990 | 1.26% | 2754 |
| chr16 | 1737139 | 1.92% | 3707 |
| chr17 | 2022590 | 2.43% | 4244 |
| chr18 | 636426 | 0.79% | 1369 |
| chr19 | 2578893 | 4.40% | 5056 |
| chr20 | 1242719 | 1.93% | 2732 |
| chr21 | 614851 | 1.32% | 1217 |
| chr22 | 1315644 | 2.59% | 2669 |
| chrX | 189597 | 0.12% | 410 |
| chrY | 17521 | 0.03% | 43 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 70129 | 150 | 3298 | 474.74 | 408 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF105ZAX.bed.gz | 2.35 MB | eaa5fc0856ac34049a0ffae92bbe71b7 |
| ENCFF105ZAX.tabix.bed.gz | 770.26 KB | 6aba2f3f0faa0b79b1415785107bbd1f |
| ENCFF105ZAX.tabix.bed.gz.tbi | 329.06 KB | 7f54080cf52a539b588bf6f0b2b7ed07 |
| genomic_resource.yaml | 4.41 KB | 3e9e40866d745d7fe119260516856d5a |
| statistics/ |