Resource
| Id | Histone_ChIP-seq/ENCSR000FCV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000FCV [biosample_summary="Homo sapiens SK-N-SH" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN863MBH|/analyses/ENCAN863MBH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF788SBY|/files/ENCFF788SBY/} processed by ChIP-seq ENCODE3 hg19 pipeline has 18139240 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF888YKS|/files/ENCFF888YKS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 30158432 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF788SBY|/files/ENCFF788SBY/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF788SBY|/files/ENCFF788SBY/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.40. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000FCV | float |
Histone_ChIP-seq_ENCSR000FCV |
Histone_ChIP-seq ENCSR000FCV [biosample_summary="Homo sapiens SK-N-SH" and target="H3K36me3"]
|
 |
[1.61, 16.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 109055931 | 3.39% | 145435 |
| chr1 | 11909264 | 4.78% | 15080 |
| chr2 | 9795247 | 4.04% | 12780 |
| chr3 | 7142645 | 3.60% | 9915 |
| chr4 | 4954859 | 2.60% | 7195 |
| chr5 | 6107813 | 3.36% | 7926 |
| chr6 | 5128894 | 3.00% | 7135 |
| chr7 | 6823345 | 4.28% | 8233 |
| chr8 | 4056578 | 2.79% | 5786 |
| chr9 | 4618077 | 3.34% | 6243 |
| chr10 | 4698280 | 3.51% | 6537 |
| chr11 | 5396711 | 4.00% | 7015 |
| chr12 | 5465223 | 4.10% | 7355 |
| chr13 | 2540480 | 2.22% | 3697 |
| chr14 | 3537078 | 3.30% | 4828 |
| chr15 | 4093262 | 4.01% | 5522 |
| chr16 | 3816394 | 4.22% | 4928 |
| chr17 | 5751018 | 6.91% | 6903 |
| chr18 | 1903710 | 2.37% | 2666 |
| chr19 | 3727332 | 6.36% | 5142 |
| chr20 | 2794700 | 4.34% | 3577 |
| chr21 | 1236758 | 2.65% | 1573 |
| chr22 | 1888895 | 3.72% | 2562 |
| chrX | 1669368 | 1.07% | 2837 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 145435 | 190 | 16140 | 749.86 | 470 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF611SDW.bed.gz | 2.98 MB | c18c9c61f88d21433d3bd7ab762b5104 |
| ENCFF611SDW.tabix.bed.gz | 1.42 MB | 679932cfc633b4c6ed2189126e95cffa |
| ENCFF611SDW.tabix.bed.gz.tbi | 170.82 KB | 07b5f59c660ec194b84520ef794d95a8 |
| genomic_resource.yaml | 3.74 KB | c2ad832a1a4b84e2fc57e30e6e7e378b |
| statistics/ |