Resource
| Id | Histone_ChIP-seq/ENCSR422LQX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR422LQX [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell male adult (21 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (21 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN189SBS|/analyses/ENCAN189SBS/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF647OUC|/files/ENCFF647OUC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 21143161 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 redacted alignments file {ENCFF647OUC|/files/ENCFF647OUC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 redacted alignments file {ENCFF647OUC|/files/ENCFF647OUC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.84. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR422LQX | float |
Histone_ChIP-seq_ENCSR422LQX |
Histone_ChIP-seq ENCSR422LQX [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell male adult (21 years)" and target="H3K4me1"]
|
 |
[1.56, 20.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 117789139 | 3.66% | 79323 |
| chr1 | 11698648 | 4.70% | 7617 |
| chr1_KI270713v1_random | 1073 | 2.63% | 2 |
| chr2 | 9914935 | 4.09% | 6508 |
| chr3 | 7443084 | 3.75% | 5063 |
| chr4 | 4143021 | 2.18% | 2958 |
| chr5 | 5942792 | 3.27% | 3891 |
| chr6 | 7189729 | 4.21% | 4913 |
| chr7 | 5465420 | 3.43% | 3804 |
| chr8 | 4507310 | 3.11% | 3114 |
| chr9 | 4463664 | 3.23% | 3036 |
| chr10 | 5445822 | 4.07% | 3613 |
| chr11 | 5888530 | 4.36% | 3782 |
| chr12 | 6019327 | 4.52% | 4093 |
| chr13 | 2805522 | 2.45% | 1926 |
| chr14 | 4679956 | 4.37% | 2855 |
| chr14_GL000194v1_random | 670 | 0.35% | 1 |
| chr15 | 3993620 | 3.92% | 2661 |
| chr16 | 4419166 | 4.89% | 2879 |
| chr17 | 6521868 | 7.83% | 4279 |
| chr17_GL000205v2_random | 1805 | 0.97% | 1 |
| chr18 | 2051688 | 2.55% | 1474 |
| chr19 | 4859308 | 8.29% | 3546 |
| chr20 | 3336264 | 5.18% | 2183 |
| chr21 | 1435116 | 3.07% | 937 |
| chr22 | 2805971 | 5.52% | 1777 |
| chrUn_GL000195v1 | 1107 | 0.61% | 2 |
| chrUn_GL000219v1 | 13725 | 7.66% | 11 |
| chrUn_GL000220v1 | 608 | 0.38% | 1 |
| chrX | 2549088 | 1.63% | 2210 |
| chrY | 190302 | 0.33% | 186 |
| 3336 contigs with no values (128135384 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 79323 | 305 | 36827 | 1484.93 | 1070 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF990JUO.bed.gz | 1.89 MB | 66dc1fa87d849694a41d49cab1edc82e |
| ENCFF990JUO.tabix.bed.gz | 862.75 KB | 69246ff46579ea73b1f050e0c46f99d3 |
| ENCFF990JUO.tabix.bed.gz.tbi | 211.76 KB | 47492415991011da6edf8bfd19f73c21 |
| genomic_resource.yaml | 3.31 KB | 746a956c65a20babfe2a1bfa1e35f835 |
| statistics/ |