Resource
| Id | ATAC-seq/ENCSR634WYX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR634WYX [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 (47 years) with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN618LZA|/analyses/ENCAN618LZA/} 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 {ENCFF786BZU|/files/ENCFF786BZU/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.749118. 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 {ENCFF786BZU|/files/ENCFF786BZU/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.77. 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 {ENCFF079ETH|/files/ENCFF079ETH/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.745163. 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 {ENCFF079ETH|/files/ENCFF079ETH/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR634WYX | float |
ATAC-seq_ENCSR634WYX |
ATAC-seq ENCSR634WYX [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.12, 43] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 88297373 | 2.74% | 136329 |
| chr1 | 9520276 | 3.82% | 14180 |
| chr2 | 6915836 | 2.86% | 11093 |
| chr3 | 5031863 | 2.54% | 8194 |
| chr4 | 3726363 | 1.96% | 6221 |
| chr5 | 4611682 | 2.54% | 7476 |
| chr6 | 4857801 | 2.84% | 7716 |
| chr7 | 4219587 | 2.65% | 6673 |
| chr8 | 3915066 | 2.70% | 6339 |
| chr9 | 3843058 | 2.78% | 5883 |
| chr10 | 4491384 | 3.36% | 7026 |
| chr11 | 4751508 | 3.52% | 7227 |
| chr12 | 3712119 | 2.79% | 5640 |
| chr13 | 2163287 | 1.89% | 3639 |
| chr14 | 2610127 | 2.44% | 4012 |
| chr15 | 2802108 | 2.75% | 4244 |
| chr16 | 3552589 | 3.93% | 5178 |
| chr17 | 4222254 | 5.07% | 5864 |
| chr18 | 2080893 | 2.59% | 3390 |
| chr19 | 3432131 | 5.86% | 4426 |
| chr20 | 2530025 | 3.93% | 3874 |
| chr21 | 1099814 | 2.35% | 1708 |
| chr22 | 1977446 | 3.89% | 2818 |
| chrX | 2134383 | 1.37% | 3320 |
| chrY | 95773 | 0.17% | 188 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136329 | 150 | 3714 | 647.68 | 554 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF305GXR.bed.gz | 5.48 MB | bc4cbbac41b062cd22766e30fbbbfe48 |
| ENCFF305GXR.tabix.bed.gz | 1.5 MB | 0b3abc4a67ffbc14f0b287236a0f0f46 |
| ENCFF305GXR.tabix.bed.gz.tbi | 518.5 KB | 04f06d6f30828de69a69e34b4ffe8616 |
| genomic_resource.yaml | 3.87 KB | 41bc84b664ec9c04ffe57c46860fc930 |
| statistics/ |