Resource
| Id | Histone_ChIP-seq/ENCSR000FCM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000FCM [biosample_summary="Homo sapiens Panc1" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN609OEA|/analyses/ENCAN609OEA/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF114KPN|/files/ENCFF114KPN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 16247909 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 {ENCFF455VTP|/files/ENCFF455VTP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15009966 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 {ENCFF114KPN|/files/ENCFF114KPN/} processed by ChIP-seq ENCODE3 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 {ENCFF114KPN|/files/ENCFF114KPN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.20. 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 {ENCFF455VTP|/files/ENCFF455VTP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF455VTP|/files/ENCFF455VTP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.44. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000FCM | float |
Histone_ChIP-seq_ENCSR000FCM |
Histone_ChIP-seq ENCSR000FCM [biosample_summary="Homo sapiens Panc1" and target="H3K36me3"]
|
 |
[1.49, 14.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 25804185 | 0.80% | 82377 |
| chr1 | 3041209 | 1.22% | 9451 |
| chr2 | 2641941 | 1.09% | 8106 |
| chr3 | 1740649 | 0.88% | 5321 |
| chr4 | 707474 | 0.37% | 2868 |
| chr5 | 1800628 | 0.99% | 5328 |
| chr6 | 1545004 | 0.90% | 4805 |
| chr7 | 1361195 | 0.85% | 4179 |
| chr8 | 808238 | 0.56% | 2632 |
| chr9 | 621048 | 0.45% | 2361 |
| chr10 | 1578351 | 1.18% | 4382 |
| chr11 | 1649672 | 1.22% | 4540 |
| chr12 | 1470228 | 1.10% | 4723 |
| chr13 | 385405 | 0.34% | 1487 |
| chr14 | 708110 | 0.66% | 2727 |
| chr15 | 993160 | 0.97% | 3100 |
| chr16 | 768324 | 0.85% | 2711 |
| chr17 | 1338454 | 1.61% | 4364 |
| chr18 | 343981 | 0.43% | 1305 |
| chr19 | 638683 | 1.09% | 2023 |
| chr20 | 700131 | 1.09% | 2220 |
| chr21 | 189273 | 0.41% | 755 |
| chr22 | 277005 | 0.55% | 1130 |
| chrUn_GL000219v1 | 145 | 0.08% | 1 |
| chrX | 495877 | 0.32% | 1858 |
| 3342 contigs with no values (186125302 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 82377 | 120 | 12777 | 313.25 | 237 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF022DZS.bed.gz | 1.5 MB | 2e5f3172dd225b1f2074e7c871c59390 |
| ENCFF022DZS.tabix.bed.gz | 770.43 KB | 36b88b0f379f560609b67ee5b1d7b150 |
| ENCFF022DZS.tabix.bed.gz.tbi | 146.24 KB | 7e6f2036422f7e7b2fede21d8a3468a3 |
| genomic_resource.yaml | 4.98 KB | 9267a82e3eba9cd5b8755c1927c8d003 |
| statistics/ |