Resource
| Id | Histone_ChIP-seq/ENCSR446ZCY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR446ZCY [biosample_summary="Homo sapiens endodermal cell originated from HUES64" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN092UUX|/analyses/ENCAN092UUX/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-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 {ENCFF347EDU|/files/ENCFF347EDU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF347EDU|/files/ENCFF347EDU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.80. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value in the range 0 - 0.5 is poor complexity, 0.5 - 0.8 is moderate complexity, and > 0.8 high complexity. NRF value > 0.8 is recommended, but > 0.5 is acceptable. ENCODE processed alignments file {ENCFF937ZPT|/files/ENCFF937ZPT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with NRF value of 0.76. 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 {ENCFF937ZPT|/files/ENCFF937ZPT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.75. 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 {ENCFF937ZPT|/files/ENCFF937ZPT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 3.93. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR446ZCY | float |
Histone_ChIP-seq_ENCSR446ZCY |
Histone_ChIP-seq ENCSR446ZCY [biosample_summary="Homo sapiens endodermal cell originated from HUES64" and target="H3K4me3"]
|
 |
[1.46, 59.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 82143836 | 2.55% | 76657 |
| chr1 | 7362070 | 2.96% | 6602 |
| chr1_KI270709v1_random | 2080 | 3.11% | 3 |
| chr1_KI270713v1_random | 1544 | 3.79% | 3 |
| chr2 | 5945412 | 2.45% | 5690 |
| chr2_KI270716v1_random | 4337 | 2.82% | 7 |
| chr3 | 5141724 | 2.59% | 4883 |
| chr4 | 4399914 | 2.31% | 4329 |
| chr4_GL000008v2_random | 4418 | 2.11% | 1 |
| chr5 | 4802731 | 2.65% | 4594 |
| chr5_GL000208v1_random | 1029 | 1.11% | 2 |
| chr6 | 4974024 | 2.91% | 4454 |
| chr7 | 4260522 | 2.67% | 4342 |
| chr8 | 3731661 | 2.57% | 3673 |
| chr9 | 3108881 | 2.25% | 2838 |
| chr10 | 3617303 | 2.70% | 3500 |
| chr11 | 4128055 | 3.06% | 3821 |
| chr12 | 4445744 | 3.34% | 4076 |
| chr13 | 2233461 | 1.95% | 2285 |
| chr14 | 2955679 | 2.76% | 2760 |
| chr14_GL000225v1_random | 7651 | 3.62% | 13 |
| chr14_KI270722v1_random | 6663 | 3.43% | 7 |
| chr14_KI270723v1_random | 412 | 1.08% | 1 |
| chr15 | 2296277 | 2.25% | 2019 |
| chr16 | 2412045 | 2.67% | 2223 |
| chr17 | 3228469 | 3.88% | 2726 |
| chr17_GL000205v2_random | 16356 | 8.81% | 19 |
| chr17_KI270729v1_random | 66554 | 23.70% | 52 |
| chr17_KI270730v1_random | 3872 | 3.44% | 7 |
| chr18 | 1886727 | 2.35% | 1881 |
| chr19 | 4583788 | 7.82% | 3956 |
| chr20 | 1884137 | 2.92% | 1657 |
| chr21 | 959872 | 2.05% | 884 |
| chr22 | 1162282 | 2.29% | 1058 |
| chr22_KI270732v1_random | 866 | 2.08% | 2 |
| chr22_KI270735v1_random | 1898 | 4.43% | 2 |
| chr22_KI270736v1_random | 12362 | 6.80% | 14 |
| chr22_KI270738v1_random | 12770 | 12.85% | 18 |
| chrUn_GL000195v1 | 295 | 0.16% | 1 |
| chrUn_GL000216v2 | 60712 | 34.38% | 24 |
| chrUn_GL000219v1 | 6649 | 3.71% | 9 |
| chrUn_GL000224v1 | 6240 | 3.47% | 9 |
| chrUn_KI270333v1 | 373 | 13.82% | 1 |
| chrUn_KI270435v1 | 664 | 0.71% | 1 |
| chrUn_KI270438v1 | 11809 | 10.50% | 17 |
| chrUn_KI270442v1 | 60603 | 15.46% | 60 |
| chrUn_KI270466v1 | 788 | 63.91% | 2 |
| chrUn_KI270467v1 | 1284 | 32.76% | 2 |
| chrUn_KI270509v1 | 329 | 14.19% | 1 |
| chrUn_KI270510v1 | 418 | 17.31% | 1 |
| chrUn_KI270512v1 | 565 | 2.49% | 1 |
| chrUn_KI270515v1 | 1674 | 26.32% | 3 |
| chrUn_KI270516v1 | 287 | 22.08% | 1 |
| chrUn_KI270519v1 | 2665 | 1.93% | 5 |
| chrUn_KI270538v1 | 2217 | 2.43% | 5 |
| chrUn_KI270584v1 | 1154 | 25.57% | 2 |
| chrUn_KI270587v1 | 888 | 29.91% | 1 |
| chrUn_KI270589v1 | 2738 | 6.16% | 2 |
| chrUn_KI270590v1 | 1334 | 28.47% | 1 |
| chrUn_KI270591v1 | 773 | 13.34% | 1 |
| chrUn_KI270744v1 | 1489 | 0.88% | 2 |
| chrUn_KI270746v1 | 3759 | 5.65% | 8 |
| chrUn_KI270749v1 | 622 | 0.39% | 1 |
| chrUn_KI270750v1 | 3737 | 2.51% | 9 |
| chrUn_KI270751v1 | 641 | 0.43% | 1 |
| chrUn_KI270756v1 | 6380 | 8.02% | 6 |
| chrUn_KI270757v1 | 3120 | 4.38% | 5 |
| chrX | 2139849 | 1.37% | 1916 |
| chrY | 156190 | 0.27% | 157 |
| 3298 contigs with no values (124630414 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 76657 | 235 | 16065 | 1071.58 | 702 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF599VIR.bed.gz | 1.82 MB | 240a2debad9ffa44547facb05233c677 |
| ENCFF599VIR.tabix.bed.gz | 831.62 KB | 9421ba24c2f9ad71e7434583f95c73cd |
| ENCFF599VIR.tabix.bed.gz.tbi | 313.43 KB | 9cc2af06e83171555f1d7f4b0eb82fa1 |
| genomic_resource.yaml | 4.52 KB | 47121ec52b7fd4556c2163afc8f4eceb |
| statistics/ |