Resource
| Id | Histone_ChIP-seq/ENCSR634MAK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR634MAK [biosample_summary="Homo sapiens HUES64" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN415XDJ|/analyses/ENCAN415XDJ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF083LRD|/files/ENCFF083LRD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11747412 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed alignments file {ENCFF230FVU|/files/ENCFF230FVU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 26056838 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF083LRD|/files/ENCFF083LRD/} 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 {ENCFF083LRD|/files/ENCFF083LRD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.06. 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 {ENCFF230FVU|/files/ENCFF230FVU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF230FVU|/files/ENCFF230FVU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.95. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR634MAK | float |
Histone_ChIP-seq_ENCSR634MAK |
Histone_ChIP-seq ENCSR634MAK [biosample_summary="Homo sapiens HUES64" and target="H3K27me3"]
|
 |
[1.37, 67.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 58397684 | 1.82% | 44881 |
| chr1 | 5556209 | 2.23% | 4355 |
| chr1_KI270713v1_random | 2180 | 5.35% | 2 |
| chr2 | 4472077 | 1.85% | 3378 |
| chr3 | 2845016 | 1.43% | 2259 |
| chr4 | 2740950 | 1.44% | 1833 |
| chr5 | 3207700 | 1.77% | 2263 |
| chr6 | 3430257 | 2.01% | 2427 |
| chr7 | 2960270 | 1.86% | 2096 |
| chr8 | 2514111 | 1.73% | 1876 |
| chr9 | 2667950 | 1.93% | 2150 |
| chr9_KI270717v1_random | 808 | 2.02% | 3 |
| chr9_KI270718v1_random | 633 | 1.66% | 1 |
| chr10 | 3031713 | 2.27% | 2202 |
| chr11 | 3388836 | 2.51% | 2779 |
| chr12 | 3049138 | 2.29% | 2342 |
| chr13 | 1452157 | 1.27% | 1020 |
| chr14 | 1874974 | 1.75% | 1341 |
| chr15 | 1958354 | 1.92% | 1519 |
| chr16 | 1771250 | 1.96% | 1463 |
| chr17 | 3049756 | 3.66% | 2374 |
| chr18 | 1244891 | 1.55% | 916 |
| chr19 | 1972910 | 3.37% | 1948 |
| chr20 | 1768292 | 2.74% | 1513 |
| chr21 | 514959 | 1.10% | 370 |
| chr22 | 1554712 | 3.06% | 1306 |
| chr22_KI270733v1_random | 2133 | 1.19% | 6 |
| chrUn_GL000219v1 | 965 | 0.54% | 2 |
| chrUn_KI270752v1 | 409 | 1.47% | 1 |
| chrX | 1326118 | 0.85% | 1103 |
| chrY | 37956 | 0.07% | 33 |
| 3336 contigs with no values (128571509 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44881 | 175 | 125410 | 1301.17 | 620 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF090XFB.bed.gz | 1.04 MB | a6943a9f4bb537dfdf00372cf24c9a27 |
| ENCFF090XFB.tabix.bed.gz | 481.59 KB | 0e5150f93a017d5209e881632a807a38 |
| ENCFF090XFB.tabix.bed.gz.tbi | 135.23 KB | ea1d156e1fb97e46050c81478f7bd727 |
| genomic_resource.yaml | 4.98 KB | 698e0f6b2348dd9fb8cbaa6688d39cec |
| statistics/ |