Resource
| Id | Histone_ChIP-seq/ENCSR586POT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR586POT [biosample_summary="Homo sapiens neutrophil male" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN317GAA|/analyses/ENCAN317GAA/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF989POG|/files/ENCFF989POG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 26462620 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 alignments file {ENCFF989POG|/files/ENCFF989POG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF989POG|/files/ENCFF989POG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.05. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR586POT | float |
Histone_ChIP-seq_ENCSR586POT |
Histone_ChIP-seq ENCSR586POT [biosample_summary="Homo sapiens neutrophil male" and target="H3K4me1"]
|
 |
[1.87, 44] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 110216046 | 3.43% | 89414 |
| chr1 | 10821979 | 4.35% | 8515 |
| chr1_KI270713v1_random | 363 | 0.89% | 1 |
| chr2 | 9032035 | 3.73% | 7144 |
| chr3 | 7094925 | 3.58% | 5889 |
| chr4 | 4007477 | 2.11% | 3412 |
| chr5 | 5488701 | 3.02% | 4450 |
| chr6 | 6518711 | 3.82% | 5317 |
| chr7 | 4715136 | 2.96% | 4171 |
| chr8 | 4625144 | 3.19% | 3755 |
| chr9 | 4645520 | 3.36% | 3804 |
| chr10 | 5318690 | 3.98% | 4157 |
| chr11 | 5420026 | 4.01% | 4286 |
| chr12 | 5709043 | 4.28% | 4682 |
| chr13 | 2290032 | 2.00% | 1954 |
| chr14 | 3622759 | 3.38% | 2884 |
| chr15 | 4077937 | 4.00% | 3157 |
| chr16 | 3985479 | 4.41% | 3230 |
| chr17 | 5663062 | 6.80% | 4524 |
| chr18 | 1833573 | 2.28% | 1538 |
| chr19 | 4868377 | 8.31% | 4187 |
| chr20 | 3540782 | 5.49% | 2618 |
| chr21 | 1393310 | 2.98% | 1035 |
| chr22 | 2463805 | 4.85% | 1863 |
| chrUn_GL000195v1 | 725 | 0.40% | 1 |
| chrX | 3078455 | 1.97% | 2840 |
| 3341 contigs with no values (186080859 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 89414 | 200 | 27292 | 1232.65 | 808 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF027ZFN.bed.gz | 1.97 MB | 6f709cfa4b3a9da2b8d125ca5283cb84 |
| ENCFF027ZFN.tabix.bed.gz | 929.4 KB | a46b700ca4561823c83375c9aca5c89f |
| ENCFF027ZFN.tabix.bed.gz.tbi | 235.61 KB | d60a3e45487d4e546c6469dece32e3ba |
| genomic_resource.yaml | 3.13 KB | 4601a16bfc8639ec15a27cc48f940219 |
| statistics/ |