Detailed view of 4512-JFI-0505
Strain
| ID | 8 |
|---|---|
| Name | F344/DuCrl |
| Type | Inbred |
| Living | False |
| Source | Charles River |
| Note |
Animal
| Animal_name | F344/DuCrl_Rat1 |
|---|---|
| Sex | M |
| Age | adolescent |
| Generation | |
| Euthanasia_date | 2018-02-01 |
| Source | Charles River |
| Note | UTHSC order 6493, strain code 002 |
Tissue
| ID | 4512-JFI-0498 |
|---|---|
| Type | spleen |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0498 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 45.6 |
| DNA_target_length | |
| DNA_extraction_facility | HudsonAlpha |
| Library_kit | 150bp_PE |
| Library_facility | HudsonAlpha |
| Sequencing_instrument | HiSeq_X10 |
| Sequencing_date | 2018-07-18 |
| Sequencing_facility | HudsonAlpha |
| Sequencing_notes | Lanes per sample: 1 |
| Raw_data_dir_name | 4512-JFI-0505 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 79 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0505.LR1 | 4512-JFI-0505.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0505_f344ducr | /data/10_TB/deepvar |
| Analysis_date | 2018-08-08 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0505.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1670294 |
| mean_dna_per_gem | 721058.5761 |
| bc_on_whitelist | 0.910169557 |
| bc_mean_qscore | 38.31527743 |
| n50_linked_reads_per_molecule | 14 |
| corrected_loaded_mass_ng | 1.696200439 |
| snps_phased | 0.878833486 |
| genes_phased_lt_100kb | 0.8353741497 |
| longest_phase_block | 1354710 |
| n50_phase_block | 136294 |
| molecule_length_mean | 38460.25239 |
| molecule_length_stddev | 44986.23843 |
| number_reads | 878637502 |
| median_insert_size | 311 |
| mean_depth | 40.03111691 |
| zero_coverage | 0.02474397848 |
| mapped_reads | 0.9506978795 |
| pcr_duplication | 0.04924445437 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9520478355 |
| r1_q30_bases_fract | 0.9003678284 |
| r2_q20_bases_fract | 0.8851439853 |
| r2_q30_bases_fract | 0.7890813411 |
| si_q20_bases_fract | 0.9667619926 |
| si_q30_bases_fract | 0.9407675268 |
| bc_q20_bases_fract | 0.9921885587 |
| bc_q30_bases_fract | 0.9773621584 |
| large_sv_calls | 2096 |
| short_deletion_calls | 36270 |
Deepvariant results
| index | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 | 4512-JFI-0505.DV1 |
| Chr | chr10 | chr11 | chr12 | chr13 | chr14 | chr15 | chr16 | chr17 | chr18 | chr19 | chr1 | chr20 | chr2 | chr3 | chr4 | chr5 | chr6 | chr7 | chr8 | chr9 | chrX | chrY |
| Biallelic_Deletion | 49507 | 36585 | 33119 | 49741 | 53865 | 43373 | 41499 | 46517 | 35869 | 30601 | 104720 | 31689 | 118699 | 76085 | 75865 | 85159 | 62671 | 65869 | 57299 | 47611 | 51628 | 157 |
| Biallelic_Insertion | 49403 | 35777 | 30835 | 48196 | 51203 | 42694 | 39009 | 43272 | 35014 | 28813 | 103004 | 29960 | 113716 | 73677 | 72718 | 80376 | 61468 | 63034 | 55547 | 46974 | 51151 | 366 |
| Biallelic_SNP | 177646 | 162696 | 120483 | 204486 | 252566 | 178231 | 168017 | 194581 | 132915 | 114578 | 441232 | 130497 | 597090 | 314235 | 321716 | 363180 | 264273 | 312361 | 225077 | 178997 | 145184 | 780 |
| Multiallelic_Complex | 1568 | 844 | 869 | 1186 | 1264 | 1156 | 1028 | 1181 | 929 | 847 | 3220 | 781 | 3107 | 1999 | 1969 | 2108 | 1659 | 1743 | 1579 | 1364 | 888 | 4 |
| Multiallelic_Deletion | 3235 | 2015 | 1818 | 2438 | 2944 | 1943 | 2006 | 2504 | 1871 | 1622 | 5579 | 1457 | 6457 | 4162 | 4286 | 4688 | 3105 | 3876 | 3216 | 2222 | 1657 | 7 |
| Multiallelic_Insertion | 5531 | 3414 | 3103 | 4220 | 4900 | 3516 | 3457 | 4377 | 3139 | 2722 | 9453 | 2497 | 11105 | 7347 | 7271 | 8002 | 5476 | 6810 | 5729 | 3836 | 2399 | 9 |
| Multiallelic_SNP | 108 | 68 | 153 | 77 | 136 | 140 | 117 | 141 | 61 | 226 | 448 | 139 | 404 | 209 | 167 | 151 | 354 | 243 | 123 | 207 | 104 | 27046 |
| RefCall | 318928 | 235637 | 208960 | 299157 | 318636 | 291155 | 250515 | 277314 | 223155 | 217038 | 796095 | 190423 | 769746 | 494677 | 470105 | 491317 | 437645 | 426954 | 356667 | 330260 | 423921 | 435 |
| Transition | 114677 | 102522 | 76391 | 119294 | 158054 | 107327 | 105818 | 125130 | 84943 | 72141 | 269999 | 83079 | 365387 | 196108 | 201052 | 226648 | 160139 | 197613 | 144115 | 108407 | 79298 | 345 |
| Transversion | 62969 | 60174 | 44092 | 85192 | 94512 | 70904 | 62199 | 69451 | 47972 | 42437 | 171233 | 47418 | 231703 | 118127 | 120664 | 136532 | 104134 | 114748 | 80962 | 70590 | 65886 |