Resource
| Id | ATAC-seq/ENCSR913OWV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR913OWV [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (55 years) with amyotrophic lateral sclerosis output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN476HEY|/analyses/ENCAN476HEY/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF874HWI|/files/ENCFF874HWI/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.776291. 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 {ENCFF874HWI|/files/ENCFF874HWI/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.79. 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 {ENCFF870LIP|/files/ENCFF870LIP/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.749319. 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 {ENCFF870LIP|/files/ENCFF870LIP/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.77. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR913OWV | float |
ATAC-seq_ENCSR913OWV |
ATAC-seq ENCSR913OWV [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.28, 42.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 111792467 | 3.47% | 175093 |
| chr1 | 10207040 | 4.10% | 15574 |
| chr2 | 9269062 | 3.83% | 14963 |
| chr3 | 7076559 | 3.57% | 11511 |
| chr4 | 5381764 | 2.83% | 9071 |
| chr5 | 6407973 | 3.53% | 10498 |
| chr6 | 6348490 | 3.72% | 10228 |
| chr7 | 5617231 | 3.53% | 8837 |
| chr8 | 5134940 | 3.54% | 8364 |
| chr9 | 4955571 | 3.58% | 7712 |
| chr10 | 5730531 | 4.28% | 9015 |
| chr11 | 6002538 | 4.44% | 9133 |
| chr12 | 5064673 | 3.80% | 7919 |
| chr13 | 3088890 | 2.70% | 5209 |
| chr14 | 3538383 | 3.31% | 5483 |
| chr15 | 3638118 | 3.57% | 5661 |
| chr16 | 3899738 | 4.32% | 5692 |
| chr17 | 4820852 | 5.79% | 6800 |
| chr18 | 2746129 | 3.42% | 4538 |
| chr19 | 3321918 | 5.67% | 4241 |
| chr20 | 3082184 | 4.78% | 4703 |
| chr21 | 1341469 | 2.87% | 2092 |
| chr22 | 2258249 | 4.44% | 3208 |
| chrX | 2732477 | 1.75% | 4400 |
| chrY | 127688 | 0.22% | 241 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 175093 | 150 | 3451 | 638.47 | 557 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF201ZDJ.bed.gz | 6.49 MB | 59f131cb6bb8a6dbb2619d3821e831d2 |
| ENCFF201ZDJ.tabix.bed.gz | 1.91 MB | 0fb24a6dad76c1139d693686d56da993 |
| ENCFF201ZDJ.tabix.bed.gz.tbi | 599.66 KB | 4f98ac2e89eb0e15fe068e25767482b2 |
| genomic_resource.yaml | 3.88 KB | fe001c517ecdd49510363b8f42a5ae2c |
| statistics/ |