Resource
| Id | Histone_ChIP-seq/ENCSR000DUQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN687DIN|/analyses/ENCAN687DIN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13184720 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17156259 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 {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 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 {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.29. 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.40. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUQ | float |
Histone_ChIP-seq_ENCSR000DUQ |
Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"]
|
 |
[2.04, 117] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 31955867 | 0.99% | 30863 |
| chr1 | 3183754 | 1.28% | 3068 |
| chr1_KI270712v1_random | 266 | 0.15% | 2 |
| chr1_KI270713v1_random | 130 | 0.32% | 1 |
| chr2 | 2137493 | 0.88% | 2031 |
| chr3 | 1797267 | 0.91% | 1683 |
| chr4 | 1313210 | 0.69% | 1198 |
| chr5 | 1508879 | 0.83% | 1375 |
| chr6 | 1901730 | 1.11% | 1764 |
| chr7 | 1509540 | 0.95% | 1507 |
| chr8 | 1204352 | 0.83% | 1149 |
| chr9 | 1311297 | 0.95% | 1299 |
| chr9_KI270717v1_random | 157 | 0.39% | 1 |
| chr10 | 1362171 | 1.02% | 1302 |
| chr11 | 1752743 | 1.30% | 1629 |
| chr12 | 1688461 | 1.27% | 1551 |
| chr13 | 622121 | 0.54% | 580 |
| chr14 | 1032315 | 0.96% | 968 |
| chr14_GL000194v1_random | 217 | 0.11% | 1 |
| chr15 | 985515 | 0.97% | 952 |
| chr16 | 1292547 | 1.43% | 1303 |
| chr17 | 1843809 | 2.21% | 1854 |
| chr17_GL000205v2_random | 1997 | 1.08% | 3 |
| chr18 | 560862 | 0.70% | 538 |
| chr19 | 2091455 | 3.57% | 2154 |
| chr20 | 831716 | 1.29% | 817 |
| chr21 | 316166 | 0.68% | 313 |
| chr22 | 726539 | 1.43% | 767 |
| chr22_KI270733v1_random | 427 | 0.24% | 2 |
| chrEBV | 248 | 0.14% | 1 |
| chrUn_GL000218v1 | 222 | 0.14% | 1 |
| chrUn_GL000219v1 | 2056 | 1.15% | 4 |
| chrUn_GL000220v1 | 242 | 0.15% | 1 |
| chrX | 975963 | 0.63% | 1044 |
| 3333 contigs with no values (184816848 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30863 | 130 | 16142 | 1035.41 | 690 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF296VDQ.bed.gz | 807.8 KB | d05fa830d1e1656170e919b36e6366de |
| ENCFF296VDQ.tabix.bed.gz | 350.49 KB | adcad9ca0b221056515d47d8e21ad67d |
| ENCFF296VDQ.tabix.bed.gz.tbi | 155.79 KB | da3b633c5229ccb239e59ce84fafa342 |
| genomic_resource.yaml | 5.1 KB | b2d9dd32217fd8637f5a895f7ef8f120 |
| statistics/ |