Detailed view of 4512-JFI-0580
Strain
| ID | 31 |
|---|---|
| Name | SS/JrHsdMcwi |
| Type | Inbred |
| Living | False |
| Source | MCW |
| Note |
Animal
| Animal_name | SS/JrHsdMcwi_Rat2 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | |
| Source | Geurts |
| Note |
Tissue
| ID | 4512-JFI-0576 |
|---|---|
| Type | spleen |
| Transfer_History | Geurts to Chen |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0576 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | |
| DNA_target_length | |
| DNA_extraction_facility | HudsonAlpha |
| Library_kit | 150bp_PE |
| Library_facility | HudsonAlpha |
| Sequencing_instrument | NovaSeq |
| Sequencing_date | 2018-10-12 |
| Sequencing_facility | HudsonAlpha |
| Sequencing_notes | S4 |
| Raw_data_dir_name | 4512-JFI-0580 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 73 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0580.LR1 | 4512-JFI-0580.SN1 | 4512-JFI-0580.DV1 |
|---|---|---|---|
| Software_name | LongRanger | Supernova | DeepVariant |
| Software_version | 2.2.2 | 2.1.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0580_dss | supernova_results/dss_denovo_multi | /data/10_TB/deepvar |
| Analysis_date | 2019-04-23 | 2019-04-25 | 2019-12-04 |
| Note | combined analysis of 4512-JFI-0579 and 4512-JFI-0580 |
LongRanger results
| Analysis_ID | 4512-JFI-0580.LR1 |
|---|---|
| instrument_ids | E00332 |
| gems_detected | 1636460 |
| mean_dna_per_gem | 538611.6794 |
| bc_on_whitelist | 0.9200607501 |
| bc_mean_qscore | 38.09540733 |
| n50_linked_reads_per_molecule | 5 |
| corrected_loaded_mass_ng | 1.267016852 |
| snps_phased | 0.87246451 |
| genes_phased_lt_100kb | 0.5721969384 |
| longest_phase_block | 396963 |
| n50_phase_block | 24864 |
| molecule_length_mean | 13642.82989 |
| molecule_length_stddev | 48745.45658 |
| number_reads | 798592332 |
| median_insert_size | 266 |
| mean_depth | 34.71902209 |
| zero_coverage | 0.02455320868 |
| mapped_reads | 0.9344458744 |
| pcr_duplication | 0.04398481951 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9277304487 |
| r1_q30_bases_fract | 0.8543361144 |
| r2_q20_bases_fract | 0.8688589783 |
| r2_q30_bases_fract | 0.7708767195 |
| si_q20_bases_fract | 0.9507079114 |
| si_q30_bases_fract | 0.9152499122 |
| bc_q20_bases_fract | 0.9898741137 |
| bc_q30_bases_fract | 0.9702828955 |
| large_sv_calls | 1966 |
| short_deletion_calls | 26574 |
Deepvariant results
| index | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.DV1 | 4512-JFI-0580.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 | 49052 | 34146 | 33546 | 46593 | 51035 | 44071 | 36733 | 44729 | 36460 | 27560 | 107614 | 31108 | 116819 | 72634 | 73952 | 81714 | 64277 | 62591 | 53717 | 48086 | 50719 | 466 |
| Biallelic_Insertion | 50714 | 34930 | 31273 | 46908 | 50480 | 44479 | 36866 | 43105 | 36663 | 27600 | 108672 | 29907 | 115002 | 73856 | 73948 | 80474 | 65085 | 62386 | 54768 | 48728 | 50587 | 653 |
| Biallelic_SNP | 176585 | 144741 | 126909 | 172798 | 240709 | 184943 | 135349 | 188146 | 141595 | 95305 | 492181 | 129785 | 600387 | 295634 | 317436 | 351126 | 270903 | 289819 | 198511 | 189308 | 136355 | 2823 |
| Multiallelic_Complex | 1653 | 841 | 947 | 1225 | 1383 | 1252 | 942 | 1182 | 966 | 843 | 3201 | 766 | 3110 | 2041 | 1993 | 2083 | 1769 | 1815 | 1576 | 1438 | 848 | 19 |
| Multiallelic_Deletion | 3288 | 1797 | 1848 | 2305 | 2708 | 2004 | 1548 | 2443 | 2022 | 1290 | 5872 | 1413 | 6504 | 4036 | 4186 | 4486 | 3445 | 3663 | 3215 | 2377 | 1409 | 27 |
| Multiallelic_Insertion | 5414 | 3146 | 3237 | 3844 | 4567 | 3603 | 2632 | 4048 | 3325 | 2138 | 9840 | 2598 | 10925 | 6898 | 6952 | 7560 | 5852 | 6315 | 5189 | 4020 | 2251 | 51 |
| Multiallelic_SNP | 108 | 77 | 139 | 78 | 140 | 158 | 85 | 157 | 69 | 176 | 466 | 150 | 438 | 199 | 153 | 152 | 230 | 222 | 112 | 215 | 95 | 2 |
| RefCall | 375799 | 276356 | 229107 | 345783 | 376975 | 350746 | 275874 | 320006 | 273562 | 232497 | 936146 | 216129 | 921997 | 581864 | 564239 | 580661 | 494694 | 495842 | 417094 | 389469 | 453631 | 26832 |
| Transition | 114566 | 91163 | 81291 | 103528 | 150058 | 112406 | 83652 | 120481 | 89985 | 58761 | 302541 | 82763 | 367599 | 184735 | 197671 | 218618 | 166719 | 182826 | 127930 | 115957 | 73652 | 1504 |
| Transversion | 62019 | 53578 | 45618 | 69270 | 90651 | 72537 | 51697 | 67665 | 51610 | 36544 | 189640 | 47022 | 232788 | 110899 | 119765 | 132508 | 104184 | 106993 | 70581 | 73351 | 62703 | 1319 |