Resource
| Id | ATAC-seq/ENCSR709QRD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR709QRD [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN966AGL|/analyses/ENCAN966AGL/} 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 {ENCFF344XTT|/files/ENCFF344XTT/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.687141. 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 {ENCFF344XTT|/files/ENCFF344XTT/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.69. 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 {ENCFF733AZN|/files/ENCFF733AZN/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.688685. 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 {ENCFF733AZN|/files/ENCFF733AZN/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.69. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR709QRD | float |
ATAC-seq_ENCSR709QRD |
ATAC-seq ENCSR709QRD [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.16, 42.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 90627944 | 2.82% | 140729 |
| chr1 | 10232901 | 4.11% | 15330 |
| chr2 | 6918956 | 2.86% | 11086 |
| chr3 | 4945696 | 2.49% | 8090 |
| chr4 | 3613172 | 1.90% | 6021 |
| chr5 | 4577399 | 2.52% | 7388 |
| chr6 | 4635765 | 2.71% | 7411 |
| chr7 | 4462342 | 2.80% | 7075 |
| chr8 | 4010620 | 2.76% | 6538 |
| chr9 | 3929252 | 2.84% | 6046 |
| chr10 | 4556738 | 3.41% | 7170 |
| chr11 | 4939412 | 3.66% | 7539 |
| chr12 | 4024577 | 3.02% | 6258 |
| chr13 | 2119603 | 1.85% | 3565 |
| chr14 | 2688593 | 2.51% | 4188 |
| chr15 | 2870173 | 2.81% | 4443 |
| chr16 | 3700284 | 4.10% | 5502 |
| chr17 | 4406955 | 5.29% | 6241 |
| chr18 | 2048890 | 2.55% | 3425 |
| chr19 | 3560576 | 6.07% | 4663 |
| chr20 | 2660469 | 4.13% | 4068 |
| chr21 | 1113724 | 2.38% | 1702 |
| chr22 | 2357023 | 4.64% | 3445 |
| chrX | 2252556 | 1.44% | 3530 |
| chrY | 2268 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 140729 | 150 | 4360 | 643.99 | 548 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF010FOR.bed.gz | 5.53 MB | a061bd58a9bb7bd2ad400cead73bceb7 |
| ENCFF010FOR.tabix.bed.gz | 1.54 MB | 16505a06ada3d7914e5bee4ea45ae587 |
| ENCFF010FOR.tabix.bed.gz.tbi | 524.29 KB | 73c17d1b5b9549276a6d03b3f2e5e465 |
| genomic_resource.yaml | 3.88 KB | 336ca3c8e2a51350456fd426e9481801 |
| statistics/ |