Resource
| Id | Histone_ChIP-seq/ENCSR000DWJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWJ [biosample_summary="Homo sapiens MCF-7" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN438KUU|/analyses/ENCAN438KUU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} 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 {ENCFF222XKD|/files/ENCFF222XKD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF222XKD|/files/ENCFF222XKD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.10. 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 {ENCFF091CNO|/files/ENCFF091CNO/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.90. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWJ | float |
Histone_ChIP-seq_ENCSR000DWJ |
Histone_ChIP-seq ENCSR000DWJ [biosample_summary="Homo sapiens MCF-7" and target="H3K4me3"]
|
 |
[1.35, 103] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41883608 | 1.30% | 42803 |
| chr1 | 3971383 | 1.60% | 3976 |
| chr2 | 2965528 | 1.22% | 2996 |
| chr3 | 2380408 | 1.20% | 2458 |
| chr4 | 1749258 | 0.92% | 1814 |
| chr5 | 2062385 | 1.14% | 2093 |
| chr6 | 2513980 | 1.47% | 2427 |
| chr7 | 2052132 | 1.29% | 2231 |
| chr8 | 1601405 | 1.10% | 1697 |
| chr9 | 1692532 | 1.22% | 1769 |
| chr10 | 1828453 | 1.37% | 1885 |
| chr11 | 2089199 | 1.55% | 2059 |
| chr12 | 2247882 | 1.69% | 2203 |
| chr13 | 865974 | 0.76% | 952 |
| chr14 | 1467378 | 1.37% | 1425 |
| chr15 | 1337314 | 1.31% | 1342 |
| chr16 | 1684734 | 1.86% | 1772 |
| chr17 | 2386548 | 2.87% | 2365 |
| chr18 | 648289 | 0.81% | 709 |
| chr19 | 2472977 | 4.22% | 2520 |
| chr20 | 1164093 | 1.81% | 1223 |
| chr21 | 511352 | 1.09% | 536 |
| chr22 | 814558 | 1.60% | 905 |
| chrX | 1374575 | 0.88% | 1443 |
| chrY | 1271 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42803 | 135 | 10662 | 978.52 | 581 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF874SPN.bed.gz | 1.01 MB | f5ec62bac19f34f141cd43a09cb75bef |
| ENCFF874SPN.tabix.bed.gz | 466.68 KB | 2309b681a62868ffe0082c74938af279 |
| ENCFF874SPN.tabix.bed.gz.tbi | 206.33 KB | b1e0166ddc2494c1da5578972e8c3d9d |
| genomic_resource.yaml | 3.53 KB | db586f7500e917bccad74927bf47230e |
| statistics/ |