Resource
| Id | Histone_ChIP-seq/ENCSR450JTP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR450JTP [biosample_summary="Homo sapiens HAP-1" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN659LXJ|/analyses/ENCAN659LXJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-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 {ENCFF639UYT|/files/ENCFF639UYT/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF639UYT|/files/ENCFF639UYT/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.16. 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 {ENCFF651JPK|/files/ENCFF651JPK/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF651JPK|/files/ENCFF651JPK/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.23. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR450JTP | float |
Histone_ChIP-seq_ENCSR450JTP |
Histone_ChIP-seq ENCSR450JTP [biosample_summary="Homo sapiens HAP-1" and target="H3K4me1"]
|
 |
[1.38, 13.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 86865974 | 2.70% | 116897 |
| chr1 | 7409858 | 2.98% | 10048 |
| chr2 | 7553747 | 3.12% | 9971 |
| chr3 | 6893779 | 3.48% | 9086 |
| chr4 | 5948510 | 3.13% | 7932 |
| chr5 | 4904009 | 2.70% | 6532 |
| chr6 | 5731920 | 3.36% | 7601 |
| chr7 | 4726344 | 2.97% | 6316 |
| chr8 | 3880618 | 2.67% | 5239 |
| chr9 | 3686467 | 2.66% | 4903 |
| chr10 | 3697625 | 2.76% | 4929 |
| chr11 | 3676048 | 2.72% | 5001 |
| chr12 | 4697138 | 3.52% | 6313 |
| chr13 | 2811765 | 2.46% | 3787 |
| chr14 | 2843175 | 2.66% | 3825 |
| chr15 | 2985660 | 2.93% | 3807 |
| chr16 | 1916631 | 2.12% | 2770 |
| chr17 | 2609141 | 3.13% | 3710 |
| chr18 | 1994926 | 2.48% | 2661 |
| chr19 | 1348632 | 2.30% | 2336 |
| chr20 | 1527212 | 2.37% | 2134 |
| chr21 | 686370 | 1.47% | 961 |
| chr22 | 1077330 | 2.12% | 1559 |
| chrX | 4259069 | 2.73% | 5476 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 116897 | 185 | 11938 | 743.1 | 574 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF086KDH.bed.gz | 2.83 MB | eba8d7a3d64a12db13d957c1c03eb053 |
| ENCFF086KDH.tabix.bed.gz | 1.24 MB | 48bfeb48be7120f9f9502a8d96ecc9a7 |
| ENCFF086KDH.tabix.bed.gz.tbi | 374.12 KB | b8cb46d53375d6a060cc7fd88ff3a8ab |
| genomic_resource.yaml | 4.0 KB | c4d43add40b6d2635bab7722cd64f48c |
| statistics/ |