Detailed view of 4512-JFI-0507
Strain
| ID | 15 |
|---|---|
| Name | LEW/Crl |
| Type | Inbred |
| Living | False |
| Source | Charles River |
| Note |
Animal
| Animal_name | LEW/Crl_Rat1 |
|---|---|
| Sex | M |
| Age | adolescent |
| Generation | |
| Euthanasia_date | 2018-02-01 |
| Source | Charles River |
| Note | UTHSC order 6490 |
Tissue
| ID | 4512-JFI-0500 |
|---|---|
| Type | spleen |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0500 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 43.8 |
| 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-0507 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 80 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0507.LR1 | 4512-JFI-0507.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0507_lewcrl | /data/10_TB/deepvar |
| Analysis_date | 2018-08-09 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0507.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1529792 |
| mean_dna_per_gem | 497270.7531 |
| bc_on_whitelist | 0.907288493 |
| bc_mean_qscore | 38.36651119 |
| n50_linked_reads_per_molecule | 16 |
| corrected_loaded_mass_ng | 1.169767475 |
| snps_phased | 0.8839788125 |
| genes_phased_lt_100kb | 0.7744151105 |
| longest_phase_block | 1375884 |
| n50_phase_block | 57508 |
| molecule_length_mean | 29579.0981 |
| molecule_length_stddev | 44225.93861 |
| number_reads | 878461548 |
| median_insert_size | 343 |
| mean_depth | 38.79649135 |
| zero_coverage | 0.0250570285 |
| mapped_reads | 0.9328831955 |
| pcr_duplication | 0.05787888805 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9417177502 |
| r1_q30_bases_fract | 0.8841550632 |
| r2_q20_bases_fract | 0.8564139384 |
| r2_q30_bases_fract | 0.7471947836 |
| si_q20_bases_fract | 0.9665939431 |
| si_q30_bases_fract | 0.941521367 |
| bc_q20_bases_fract | 0.9925661349 |
| bc_q30_bases_fract | 0.9787399872 |
| large_sv_calls | 2501 |
| short_deletion_calls | 33814 |
Deepvariant results
| index | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.DV1 | 4512-JFI-0507.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 | 51267 | 29263 | 33772 | 38246 | 50463 | 40652 | 33089 | 45460 | 30773 | 27643 | 97735 | 29963 | 115481 | 76036 | 72548 | 82806 | 63215 | 59577 | 53333 | 46193 | 44442 | 152 |
| Biallelic_Insertion | 50587 | 30422 | 30646 | 38736 | 49087 | 40870 | 32397 | 43144 | 31227 | 26494 | 98256 | 28572 | 111323 | 74314 | 71084 | 79193 | 62284 | 58216 | 53035 | 46100 | 43952 | 345 |
| Biallelic_SNP | 182868 | 102531 | 125514 | 92485 | 228132 | 156270 | 97626 | 188208 | 93322 | 92210 | 397437 | 118408 | 572605 | 315604 | 299327 | 349242 | 268830 | 257897 | 197399 | 168544 | 107908 | 787 |
| Multiallelic_Complex | 1560 | 789 | 935 | 1011 | 1333 | 1092 | 826 | 1149 | 797 | 831 | 3013 | 721 | 2877 | 2039 | 1788 | 2088 | 1603 | 1653 | 1444 | 1266 | 664 | 9 |
| Multiallelic_Deletion | 3396 | 1307 | 1817 | 1430 | 2568 | 1698 | 1154 | 2530 | 1347 | 1343 | 4753 | 1225 | 6133 | 4360 | 4126 | 4312 | 3237 | 3428 | 2912 | 1998 | 820 | 7 |
| Multiallelic_Insertion | 6041 | 2250 | 3247 | 2208 | 4336 | 2671 | 2061 | 4349 | 2236 | 2223 | 8085 | 2234 | 10803 | 7353 | 6631 | 7690 | 5648 | 5907 | 4925 | 3735 | 1490 | 10 |
| Multiallelic_SNP | 112 | 61 | 142 | 48 | 147 | 135 | 72 | 138 | 52 | 199 | 387 | 127 | 482 | 219 | 137 | 145 | 329 | 207 | 109 | 173 | 78 | 23153 |
| RefCall | 315285 | 211840 | 204133 | 265073 | 308647 | 282955 | 218065 | 277739 | 205752 | 197795 | 768215 | 183503 | 757498 | 485184 | 454257 | 474639 | 434938 | 406317 | 347342 | 324987 | 364098 | 453 |
| Transition | 118675 | 62890 | 80155 | 52789 | 141560 | 92939 | 58803 | 120849 | 57837 | 56502 | 239512 | 74416 | 350560 | 196967 | 185458 | 217184 | 162003 | 161141 | 125731 | 101538 | 56836 | 334 |
| Transversion | 64193 | 39641 | 45359 | 39696 | 86572 | 63331 | 38823 | 67359 | 35485 | 35708 | 157925 | 43992 | 222045 | 118637 | 113869 | 132058 | 106827 | 96756 | 71668 | 67006 | 51072 |