Resource
| Id | ATAC-seq/ENCSR419UYY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR419UYY [biosample_summary="Homo sapiens GM19025"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN836ESF|/analyses/ENCAN836ESF/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF462RHM|/files/ENCFF462RHM/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24810004 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. 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 {ENCFF462RHM|/files/ENCFF462RHM/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.872127. 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 {ENCFF462RHM|/files/ENCFF462RHM/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR419UYY | float |
ATAC-seq_ENCSR419UYY |
ATAC-seq ENCSR419UYY [biosample_summary="Homo sapiens GM19025"]
|
 |
[1.45, 39] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48784980 | 1.52% | 89483 |
| chr1 | 4305965 | 1.73% | 7781 |
| chr2 | 4275516 | 1.77% | 7971 |
| chr3 | 3453844 | 1.74% | 6441 |
| chr4 | 2916871 | 1.53% | 5558 |
| chr5 | 3012520 | 1.66% | 5633 |
| chr6 | 3273638 | 1.92% | 6037 |
| chr7 | 2710964 | 1.70% | 5039 |
| chr8 | 2413855 | 1.66% | 4507 |
| chr9 | 1901406 | 1.37% | 3494 |
| chr10 | 2337071 | 1.75% | 4292 |
| chr11 | 2331697 | 1.73% | 4282 |
| chr12 | 2418872 | 1.81% | 4409 |
| chr13 | 1388050 | 1.21% | 2596 |
| chr14 | 1500422 | 1.40% | 2718 |
| chr15 | 1353620 | 1.33% | 2455 |
| chr16 | 1353847 | 1.50% | 2340 |
| chr17 | 1650897 | 1.98% | 2861 |
| chr18 | 1148224 | 1.43% | 2175 |
| chr19 | 1266178 | 2.16% | 2067 |
| chr20 | 1021296 | 1.58% | 1918 |
| chr21 | 489915 | 1.05% | 860 |
| chr22 | 632636 | 1.24% | 1069 |
| chrX | 1505566 | 0.96% | 2738 |
| chrY | 122110 | 0.21% | 242 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 89483 | 150 | 2821 | 545.19 | 475 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF915OAM.bed.gz | 3.36 MB | d3f34db061b4ebd4759b32bac088543c |
| ENCFF915OAM.tabix.bed.gz | 1002.67 KB | 364634102038dd146fa9e94d5410b019 |
| ENCFF915OAM.tabix.bed.gz.tbi | 417.71 KB | e1626bc6dcbb14f9c85f69750352640f |
| genomic_resource.yaml | 2.86 KB | 4b4306d59b50592ca70d40f706270118 |
| statistics/ |