Resource
| Id | Histone_ChIP-seq/ENCSR000AOU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AOU [biosample_summary="Homo sapiens astrocyte" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN144PPN|/analyses/ENCAN144PPN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF025QGZ|/files/ENCFF025QGZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7951862 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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: Processed alignments file {ENCFF962TLU|/files/ENCFF962TLU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13999561 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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 {ENCFF962TLU|/files/ENCFF962TLU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF962TLU|/files/ENCFF962TLU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.29. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AOU | float |
Histone_ChIP-seq_ENCSR000AOU |
Histone_ChIP-seq ENCSR000AOU [biosample_summary="Homo sapiens astrocyte" and target="H3K4me3"]
|
 |
[2.09, 67] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41693516 | 1.30% | 39108 |
| chr1 | 4020117 | 1.61% | 3664 |
| chr1_KI270713v1_random | 352 | 0.86% | 1 |
| chr2 | 3000977 | 1.24% | 2873 |
| chr3 | 2540624 | 1.28% | 2297 |
| chr4 | 1858366 | 0.98% | 1702 |
| chr5 | 2197946 | 1.21% | 2004 |
| chr6 | 2605138 | 1.53% | 2353 |
| chr7 | 1990424 | 1.25% | 1907 |
| chr8 | 1675499 | 1.15% | 1628 |
| chr9 | 1686484 | 1.22% | 1616 |
| chr10 | 1854325 | 1.39% | 1810 |
| chr11 | 2187304 | 1.62% | 1971 |
| chr12 | 2213390 | 1.66% | 2027 |
| chr13 | 966748 | 0.85% | 957 |
| chr14 | 1332420 | 1.24% | 1222 |
| chr15 | 1383590 | 1.36% | 1313 |
| chr16 | 1501229 | 1.66% | 1447 |
| chr17 | 2168483 | 2.60% | 2059 |
| chr17_GL000205v2_random | 2117 | 1.14% | 2 |
| chr17_KI270729v1_random | 303 | 0.11% | 1 |
| chr18 | 815277 | 1.01% | 817 |
| chr19 | 2159176 | 3.68% | 2029 |
| chr20 | 1009471 | 1.57% | 958 |
| chr21 | 426493 | 0.91% | 412 |
| chr22 | 836062 | 1.65% | 820 |
| chrUn_GL000195v1 | 983 | 0.54% | 3 |
| chrUn_GL000219v1 | 3706 | 2.07% | 4 |
| chrUn_KI270438v1 | 1606 | 1.43% | 4 |
| chrX | 1214377 | 0.78% | 1184 |
| chrY | 40529 | 0.07% | 23 |
| 3336 contigs with no values (128095311 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39108 | 180 | 14078 | 1066.11 | 681 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF375FQE.bed.gz | 1.01 MB | bb9ea5040d1601a5f1c1334a776edabe |
| ENCFF375FQE.tabix.bed.gz | 440.58 KB | bcc32e48926f2f8b3a9d05897e8754d1 |
| ENCFF375FQE.tabix.bed.gz.tbi | 200.59 KB | 6e62809f6f096a51b1b2f2b563312869 |
| genomic_resource.yaml | 3.68 KB | 9f55022ef92e7aa638b1509120442fca |
| statistics/ |