Detailed view of 95-39696
Strain
| ID | 4 |
|---|---|
| Name | BN/NHsdMcwi |
| Type | Inbred |
| Living | False |
| Source | MCW |
| Note |
Animal
| Animal_name | BN/NHsdMcwi_Rat2 |
|---|---|
| Sex | M |
| Age | weaning |
| Generation | |
| Euthanasia_date | 2018-03-01 |
| Source | Dwinell |
| Note |
Tissue
| ID | 95-38313 |
|---|---|
| Type | kidney |
| Transfer_History | Dwinell to chen to Dalgard |
| Note | None |
Sequencing
| DNA_source | 95-38313 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | |
| DNA_target_length | |
| DNA_extraction_facility | USUHS |
| Library_kit | 150bp_PE |
| Library_facility | USUHS |
| Sequencing_instrument | HiSeq_X |
| Sequencing_date | 2019-09-01 |
| Sequencing_facility | USUHS |
| Sequencing_notes | |
| Raw_data_dir_name | 95-39696 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 60 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39696.LR1 | 95-39696.GH1 | 95-39696.DV1 |
|---|---|---|---|
| Software_name | LongRanger | GROC-SVs | DeepVariant |
| Software_version | 2.2.2 | Udit_PR3 | 0.9.0-gpu |
| Results_dir | longranger_results/BN_male | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-03 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39696.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1813273 |
| mean_dna_per_gem | 682219.9227 |
| bc_on_whitelist | 0.9229319497 |
| bc_mean_qscore | 36.30744491 |
| n50_linked_reads_per_molecule | 8 |
| corrected_loaded_mass_ng | 1.604837348 |
| snps_phased | 0.8629907469 |
| genes_phased_lt_100kb | 0.770065917 |
| longest_phase_block | 949082 |
| n50_phase_block | 35379 |
| molecule_length_mean | 23447.8862 |
| molecule_length_stddev | 36486.98174 |
| number_reads | 819416344 |
| median_insert_size | 358 |
| mean_depth | 36.18721968 |
| zero_coverage | 0.02029100015 |
| mapped_reads | 0.9295955708 |
| pcr_duplication | 0.04395423818 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9420984011 |
| r1_q30_bases_fract | 0.8924078396 |
| r2_q20_bases_fract | 0.9221191185 |
| r2_q30_bases_fract | 0.8612254893 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9859719219 |
| bc_q30_bases_fract | 0.9590621785 |
| large_sv_calls | 1900 |
| short_deletion_calls | 19131 |
Deepvariant results
| index | 331 | 332 | 333 | 334 | 335 | 336 | 337 | 338 | 339 | 340 | 341 | 342 | 343 | 344 | 345 | 346 | 347 | 348 | 349 | 350 | 351 | 352 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.DV1 | 95-39696.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 | 26167 | 17619 | 19848 | 28068 | 26575 | 26123 | 23372 | 24522 | 19991 | 18612 | 60415 | 17446 | 56421 | 40430 | 38525 | 43717 | 35319 | 32776 | 29917 | 29184 | 35840 | 413 |
| Biallelic_Insertion | 29600 | 19507 | 19815 | 29187 | 27921 | 26953 | 23454 | 24802 | 21331 | 18639 | 64077 | 17758 | 59996 | 42777 | 40897 | 45434 | 37360 | 35798 | 32381 | 30183 | 34914 | 555 |
| Biallelic_SNP | 25929 | 19844 | 30033 | 26853 | 39714 | 44744 | 30550 | 29035 | 19198 | 31440 | 111967 | 17016 | 94245 | 49992 | 40618 | 46965 | 47139 | 68287 | 35852 | 41879 | 52009 | 2682 |
| Multiallelic_Complex | 657 | 381 | 422 | 545 | 583 | 584 | 433 | 463 | 382 | 387 | 1549 | 331 | 1219 | 915 | 792 | 829 | 733 | 863 | 707 | 658 | 405 | 10 |
| Multiallelic_Deletion | 203 | 120 | 118 | 196 | 206 | 206 | 138 | 176 | 155 | 128 | 475 | 101 | 458 | 297 | 290 | 276 | 246 | 280 | 232 | 216 | 145 | 18 |
| Multiallelic_Insertion | 815 | 418 | 559 | 582 | 639 | 631 | 491 | 563 | 458 | 513 | 1637 | 401 | 1301 | 957 | 913 | 995 | 830 | 990 | 790 | 704 | 381 | 40 |
| Multiallelic_SNP | 25 | 15 | 43 | 18 | 31 | 78 | 23 | 45 | 21 | 55 | 153 | 10 | 157 | 37 | 16 | 22 | 75 | 103 | 34 | 59 | 30 | 1 |
| RefCall | 277864 | 189480 | 175974 | 251509 | 254702 | 265402 | 204419 | 225458 | 187863 | 189809 | 689714 | 148724 | 602001 | 400737 | 380415 | 390146 | 336267 | 363349 | 301866 | 287407 | 337559 | 26350 |
| Transition | 11162 | 8790 | 14119 | 11054 | 18136 | 21323 | 13860 | 12895 | 8100 | 15043 | 52955 | 7030 | 43815 | 22425 | 17649 | 20610 | 20859 | 34123 | 15769 | 19194 | 23369 | 1399 |
| Transversion | 14767 | 11054 | 15914 | 15799 | 21578 | 23421 | 16690 | 16140 | 11098 | 16397 | 59012 | 9986 | 50430 | 27567 | 22969 | 26355 | 26280 | 34164 | 20083 | 22685 | 28640 | 1283 |