Resource
| Id | ATAC-seq/ENCSR673ZMQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR673ZMQ [biosample_summary="Homo sapiens HG03025"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN812ZXZ|/analyses/ENCAN812ZXZ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN812ZXZ|/analyses/ENCAN812ZXZ/} has in progress subobject document {afafb2e9-319b-4962-a498-10d19619de67|/documents/afafb2e9-319b-4962-a498-10d19619de67/} audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF535JYQ|/files/ENCFF535JYQ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.18. 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 {ENCFF715RQC|/files/ENCFF715RQC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.841704. 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 {ENCFF715RQC|/files/ENCFF715RQC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR673ZMQ | float |
ATAC-seq_ENCSR673ZMQ |
ATAC-seq ENCSR673ZMQ [biosample_summary="Homo sapiens HG03025"]
|
 |
[1.32, 27.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 44656903 | 1.39% | 84750 |
| chr1 | 3979594 | 1.60% | 7413 |
| chr2 | 4000593 | 1.65% | 7814 |
| chr3 | 3257819 | 1.64% | 6428 |
| chr4 | 2707983 | 1.42% | 5486 |
| chr5 | 2811207 | 1.55% | 5580 |
| chr6 | 2998025 | 1.76% | 5757 |
| chr7 | 2518355 | 1.58% | 4860 |
| chr8 | 2244318 | 1.55% | 4493 |
| chr9 | 1683282 | 1.22% | 3190 |
| chr10 | 2059095 | 1.54% | 3951 |
| chr11 | 2172515 | 1.61% | 4098 |
| chr12 | 2213137 | 1.66% | 4128 |
| chr13 | 1306219 | 1.14% | 2551 |
| chr14 | 1312694 | 1.23% | 2393 |
| chr15 | 1161315 | 1.14% | 2094 |
| chr16 | 1219328 | 1.35% | 2068 |
| chr17 | 1422921 | 1.71% | 2338 |
| chr18 | 999488 | 1.24% | 2010 |
| chr19 | 1203301 | 2.05% | 1814 |
| chr20 | 879867 | 1.37% | 1639 |
| chr21 | 412142 | 0.88% | 721 |
| chr22 | 514020 | 1.01% | 835 |
| chrX | 1579402 | 1.01% | 3088 |
| chrY | 283 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84750 | 150 | 3506 | 526.93 | 427 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF535JYQ.bed.gz | 3.08 MB | 6f7f7acd528a877051836ab887122abd |
| ENCFF535JYQ.tabix.bed.gz | 928.33 KB | e5a77e59c8014140589c5b2794770b77 |
| ENCFF535JYQ.tabix.bed.gz.tbi | 423.49 KB | 053d8db9451cf45d629caf7923a2aa77 |
| genomic_resource.yaml | 3.13 KB | 8f353cf58b861e6074a1550a455d738d |
| statistics/ |