Resource
| Id | ATAC-seq/ENCSR410DWV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR410DWV [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male child (6 years) with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN032WVS|/analyses/ENCAN032WVS/} 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 {ENCFF628IGU|/files/ENCFF628IGU/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.750725. 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 {ENCFF628IGU|/files/ENCFF628IGU/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.76. 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 {ENCFF789NRH|/files/ENCFF789NRH/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.756094. 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 {ENCFF789NRH|/files/ENCFF789NRH/} 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_ENCSR410DWV | float |
ATAC-seq_ENCSR410DWV |
ATAC-seq ENCSR410DWV [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.48, 41.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 134683376 | 4.19% | 184639 |
| chr1 | 12559571 | 5.04% | 16980 |
| chr2 | 11316119 | 4.67% | 15770 |
| chr3 | 9210966 | 4.65% | 12811 |
| chr4 | 6762924 | 3.56% | 9665 |
| chr5 | 7588905 | 4.18% | 10643 |
| chr6 | 8065638 | 4.72% | 11093 |
| chr7 | 7020636 | 4.41% | 9756 |
| chr8 | 6264879 | 4.32% | 8787 |
| chr9 | 5756248 | 4.16% | 7816 |
| chr10 | 6553507 | 4.90% | 8995 |
| chr11 | 6910308 | 5.12% | 9302 |
| chr12 | 6521941 | 4.89% | 8975 |
| chr13 | 3340779 | 2.92% | 4760 |
| chr14 | 3997054 | 3.73% | 5497 |
| chr15 | 4501449 | 4.41% | 6119 |
| chr16 | 4342593 | 4.81% | 5701 |
| chr17 | 5577078 | 6.70% | 7229 |
| chr18 | 3111625 | 3.87% | 4415 |
| chr19 | 3964441 | 6.76% | 4885 |
| chr20 | 3827067 | 5.94% | 5217 |
| chr21 | 1638035 | 3.51% | 2224 |
| chr22 | 2515831 | 4.95% | 3246 |
| chrX | 3163032 | 2.03% | 4480 |
| chrY | 172750 | 0.30% | 273 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 184639 | 150 | 4812 | 729.44 | 653 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF610SOB.bed.gz | 7.09 MB | 5aeeb06e63f3694bb627f9c4e98e3d06 |
| ENCFF610SOB.tabix.bed.gz | 2.05 MB | 5bc2af0a833eff84a14a5aab41dd7015 |
| ENCFF610SOB.tabix.bed.gz.tbi | 595.5 KB | 3919a4e6104a9e300d3749a3afa05a49 |
| genomic_resource.yaml | 3.87 KB | 3829b9ddf628c419570840ed79e6c298 |
| statistics/ |