Resource
| Id | Histone_ChIP-seq/ENCSR150GLE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR150GLE [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN850BOT|/analyses/ENCAN850BOT/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF715RSO|/files/ENCFF715RSO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 32026620 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF462ZPE|/files/ENCFF462ZPE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF462ZPE|/files/ENCFF462ZPE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.44. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR150GLE | float |
Histone_ChIP-seq_ENCSR150GLE |
Histone_ChIP-seq ENCSR150GLE [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K9me3"]
|
 |
[1.47, 40.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 21516281 | 0.67% | 68023 |
| chr1 | 1260159 | 0.51% | 4125 |
| chr2 | 1630074 | 0.67% | 5407 |
| chr3 | 1130813 | 0.57% | 3745 |
| chr4 | 1406491 | 0.74% | 4433 |
| chr5 | 1318742 | 0.73% | 4186 |
| chr6 | 1011965 | 0.59% | 3375 |
| chr7 | 1367028 | 0.86% | 4210 |
| chr8 | 1218898 | 0.84% | 3852 |
| chr9 | 708703 | 0.51% | 2252 |
| chr10 | 1126270 | 0.84% | 3649 |
| chr11 | 886742 | 0.66% | 2914 |
| chr12 | 1071415 | 0.80% | 3154 |
| chr13 | 781612 | 0.68% | 2498 |
| chr14 | 590235 | 0.55% | 1952 |
| chr15 | 600316 | 0.59% | 1725 |
| chr16 | 702844 | 0.78% | 2183 |
| chr17 | 410412 | 0.49% | 1335 |
| chr18 | 551349 | 0.69% | 1860 |
| chr19 | 1936276 | 3.30% | 5212 |
| chr20 | 476189 | 0.74% | 1571 |
| chr21 | 406389 | 0.87% | 1252 |
| chr22 | 272669 | 0.54% | 900 |
| chrX | 569538 | 0.36% | 1987 |
| chrY | 81152 | 0.14% | 246 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 68023 | 135 | 16362 | 316.31 | 260 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF235VTD.bed.gz | 1.24 MB | 6d0a8f22299c8cf517c141dd3e319756 |
| ENCFF235VTD.tabix.bed.gz | 644.41 KB | 6018554210584f5fa882186680a57bc4 |
| ENCFF235VTD.tabix.bed.gz.tbi | 330.72 KB | 1012c1feba6c32e67fe8f9e2d02fb56e |
| genomic_resource.yaml | 3.23 KB | aff3c29e98bbf1d8651043c149ed0aea |
| statistics/ |