Detailed view of 4512-JFI-0503
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 | 4512-JFI-0496 |
|---|---|
| Type | liver |
| Transfer_History | Dwinell to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0496 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 38.6 |
| 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-0503 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 80 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0503.LR1 | 4512-JFI-0503.GH1 | 4512-JFI-0503.DV1 |
|---|---|---|---|
| Software_name | LongRanger | GROC-SVs | DeepVariant |
| Software_version | 2.2.2 | Udit_PR3 | 0.9.0-gpu |
| Results_dir | longranger_results/0503_bn_male | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2018-08-01 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 4512-JFI-0503.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1668604 |
| mean_dna_per_gem | 713110.7428 |
| bc_on_whitelist | 0.9043519828 |
| bc_mean_qscore | 38.45837964 |
| n50_linked_reads_per_molecule | 11 |
| corrected_loaded_mass_ng | 1.677504152 |
| snps_phased | 0.8520818865 |
| genes_phased_lt_100kb | 0.8002915452 |
| longest_phase_block | 1902604 |
| n50_phase_block | 66781 |
| molecule_length_mean | 34028.84304 |
| molecule_length_stddev | 42354.43298 |
| number_reads | 894179226 |
| median_insert_size | 298 |
| mean_depth | 40.53812988 |
| zero_coverage | 0.02050646205 |
| mapped_reads | 0.9488682351 |
| pcr_duplication | 0.05687927765 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9485948979 |
| r1_q30_bases_fract | 0.8932050275 |
| r2_q20_bases_fract | 0.8837673889 |
| r2_q30_bases_fract | 0.789519365 |
| si_q20_bases_fract | 0.9692865662 |
| si_q30_bases_fract | 0.9458797522 |
| bc_q20_bases_fract | 0.993075772 |
| bc_q30_bases_fract | 0.9814167714 |
| large_sv_calls | 1740 |
| short_deletion_calls | 16894 |
Deepvariant results
| index | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.DV1 | 4512-JFI-0503.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 | 28672 | 19375 | 21506 | 30415 | 28778 | 28535 | 25230 | 26372 | 21740 | 19919 | 65742 | 18796 | 61065 | 43905 | 42033 | 47260 | 38255 | 35576 | 32973 | 31645 | 38509 | 436 |
| Biallelic_Insertion | 34458 | 22936 | 22250 | 33692 | 31921 | 31221 | 26838 | 28016 | 24552 | 21251 | 73787 | 20068 | 69128 | 49415 | 47202 | 52095 | 42738 | 40872 | 37223 | 34750 | 40072 | 591 |
| Biallelic_SNP | 26092 | 20160 | 30435 | 27016 | 39874 | 44763 | 30904 | 29743 | 19391 | 32361 | 113865 | 17305 | 94801 | 50815 | 41173 | 47325 | 47398 | 69005 | 36193 | 42738 | 52662 | 2703 |
| Multiallelic_Complex | 1146 | 642 | 592 | 867 | 926 | 905 | 752 | 784 | 671 | 636 | 2314 | 523 | 2008 | 1420 | 1353 | 1387 | 1229 | 1254 | 1056 | 1025 | 626 | 19 |
| Multiallelic_Deletion | 325 | 207 | 180 | 346 | 325 | 322 | 244 | 285 | 225 | 196 | 829 | 154 | 699 | 488 | 478 | 449 | 374 | 414 | 383 | 367 | 235 | 19 |
| Multiallelic_Insertion | 1126 | 592 | 726 | 809 | 846 | 825 | 682 | 732 | 600 | 642 | 2240 | 574 | 1721 | 1395 | 1215 | 1282 | 1117 | 1294 | 1009 | 957 | 496 | 57 |
| Multiallelic_SNP | 20 | 25 | 37 | 25 | 50 | 84 | 47 | 59 | 26 | 77 | 172 | 15 | 184 | 41 | 32 | 40 | 96 | 113 | 46 | 81 | 40 | 3 |
| RefCall | 272798 | 196217 | 172077 | 256974 | 259516 | 270854 | 208077 | 226910 | 191121 | 190304 | 700380 | 149227 | 618352 | 405421 | 390609 | 398297 | 338712 | 364835 | 303390 | 294226 | 355991 | 26759 |
| Transition | 11328 | 9035 | 14382 | 11252 | 18321 | 21542 | 14089 | 13316 | 8304 | 15639 | 54156 | 7310 | 44506 | 22999 | 18141 | 20916 | 21143 | 34692 | 16139 | 19740 | 24456 | 1395 |
| Transversion | 14764 | 11125 | 16053 | 15764 | 21553 | 23221 | 16815 | 16427 | 11087 | 16722 | 59709 | 9995 | 50295 | 27816 | 23032 | 26409 | 26255 | 34313 | 20054 | 22998 | 28206 | 1308 |