Resource
| Id | Histone_ChIP-seq/ENCSR000AMX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AMX [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K9ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female child (11 years) male adult (45 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN671XSS|/analyses/ENCAN671XSS/} has in progress subobject document {eed75a14-d170-40b2-8452-2b205cd75b38|/documents/eed75a14-d170-40b2-8452-2b205cd75b38/} audit_internal_action: Released analysis {ENCAN671XSS|/analyses/ENCAN671XSS/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF893NLT|/files/ENCFF893NLT/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 5656242 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed alignments file {ENCFF928PXO|/files/ENCFF928PXO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 8641616 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) 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 > 0.8 is acceptable. ENCODE processed alignments file {ENCFF928PXO|/files/ENCFF928PXO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 alignments file {ENCFF928PXO|/files/ENCFF928PXO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.62. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AMX | float |
Histone_ChIP-seq_ENCSR000AMX |
Histone_ChIP-seq ENCSR000AMX [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K9ac"]
|
 |
[2.06, 111] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 22089167 | 0.69% | 33987 |
| chr1 | 2163179 | 0.87% | 3383 |
| chr2 | 1524446 | 0.63% | 2322 |
| chr3 | 1228273 | 0.62% | 1821 |
| chr4 | 773211 | 0.41% | 1115 |
| chr5 | 1065709 | 0.59% | 1619 |
| chr6 | 1197988 | 0.70% | 1793 |
| chr7 | 1045129 | 0.66% | 1585 |
| chr8 | 853182 | 0.59% | 1307 |
| chr9 | 937663 | 0.68% | 1503 |
| chr10 | 960267 | 0.72% | 1515 |
| chr11 | 1305945 | 0.97% | 1931 |
| chr12 | 1178736 | 0.88% | 1737 |
| chr13 | 440010 | 0.38% | 716 |
| chr14 | 683111 | 0.64% | 1003 |
| chr15 | 717359 | 0.70% | 1076 |
| chr16 | 986462 | 1.09% | 1571 |
| chr17 | 1386037 | 1.66% | 2175 |
| chr18 | 338641 | 0.42% | 524 |
| chr19 | 1415668 | 2.42% | 2199 |
| chr20 | 572456 | 0.89% | 869 |
| chr21 | 246302 | 0.53% | 401 |
| chr22 | 532693 | 1.05% | 862 |
| chrX | 523403 | 0.34% | 936 |
| chrY | 13297 | 0.02% | 24 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33987 | 140 | 12050 | 649.93 | 441 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF635CCP.bed.gz | 764.81 KB | cf603aa9e643e394116c8c8be7844c1d |
| ENCFF635CCP.tabix.bed.gz | 356.51 KB | 8e40ec0426e1a9383827bc0075457b7f |
| ENCFF635CCP.tabix.bed.gz.tbi | 149.38 KB | e18916d5cd32011516de0885b0c4cc1a |
| genomic_resource.yaml | 4.09 KB | 5ea36b60cbee31ed39be2451a2e4ad5d |
| statistics/ |