Resource
| Id | ATAC-seq/ENCSR131HOY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR131HOY [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: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN046FVR|/analyses/ENCAN046FVR/} 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 {ENCFF347EQI|/files/ENCFF347EQI/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.460297. 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 {ENCFF347EQI|/files/ENCFF347EQI/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.42. 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 {ENCFF275GRM|/files/ENCFF275GRM/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.455439. 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 {ENCFF275GRM|/files/ENCFF275GRM/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.42. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed file {ENCFF347EQI|/files/ENCFF347EQI/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.55. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed file {ENCFF275GRM|/files/ENCFF275GRM/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.52. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR131HOY | float |
ATAC-seq_ENCSR131HOY |
ATAC-seq ENCSR131HOY [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.26, 40.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 106108053 | 3.30% | 154414 |
| chr1 | 9700753 | 3.90% | 13971 |
| chr2 | 9214952 | 3.80% | 13588 |
| chr3 | 7003576 | 3.53% | 10290 |
| chr4 | 5722682 | 3.01% | 8516 |
| chr5 | 6114994 | 3.37% | 9086 |
| chr6 | 6417987 | 3.76% | 9306 |
| chr7 | 5763473 | 3.62% | 8349 |
| chr8 | 5176760 | 3.57% | 7555 |
| chr9 | 4424519 | 3.20% | 6396 |
| chr10 | 5385777 | 4.03% | 7885 |
| chr11 | 5675480 | 4.20% | 8127 |
| chr12 | 5298783 | 3.98% | 7670 |
| chr13 | 2649815 | 2.32% | 4060 |
| chr14 | 3141635 | 2.93% | 4586 |
| chr15 | 3183044 | 3.12% | 4677 |
| chr16 | 3404241 | 3.77% | 4815 |
| chr17 | 3929261 | 4.72% | 5519 |
| chr18 | 2416215 | 3.01% | 3714 |
| chr19 | 3008877 | 5.13% | 3980 |
| chr20 | 2545972 | 3.95% | 3736 |
| chr21 | 1067699 | 2.29% | 1571 |
| chr22 | 1531955 | 3.01% | 2201 |
| chrX | 3326324 | 2.13% | 4807 |
| chrY | 3279 | 0.01% | 9 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 154414 | 150 | 4282 | 687.17 | 616 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF497ACM.bed.gz | 5.95 MB | 3b19070c6f50754d2586086d492d9c62 |
| ENCFF497ACM.tabix.bed.gz | 1.68 MB | 8689f2393012434e9968a7016d495583 |
| ENCFF497ACM.tabix.bed.gz.tbi | 569.03 KB | 87cd717998d340a10f044215ec9a61aa |
| genomic_resource.yaml | 5.11 KB | 8254a619591ab7cb842a7a9ae55c009c |
| statistics/ |