Detailed view of 4512-JFI-0582
Strain
| ID | 11 |
|---|---|
| Name | FHH/EurMcwi |
| Type | Inbred |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | FHH/EurMcwi_Rat2 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | None |
| Euthanasia_date | None |
| Source | Geurts |
| Note | None |
Tissue
| ID | 4512-JFI-0578 |
|---|---|
| Type | spleen |
| Transfer_History | Geurts to Chen |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0578 |
|---|---|
| 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-0582 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 73 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0582.LR1 | 4512-JFI-0582.SN2 | 4512-JFI-0582.DV1 |
|---|---|---|---|
| Software_name | LongRanger | Supernova | DeepVariant |
| Software_version | 2.2.2 | 2.1.1 | 0.9.0-gpu |
| Results_dir | longranger_results/0582_fhh | supernova_results/fhh_denovo_multi | /data/10_TB/deepvar |
| Analysis_date | 2019-03-29 | 2019-04-27 | 2019-12-04 |
| Note | combined analysis of 4512-JFI-0581 and 4512-JFI-0582 |
LongRanger results
| Analysis_ID | 4512-JFI-0582.LR1 |
|---|---|
| instrument_ids | E00332 |
| gems_detected | 1638699 |
| mean_dna_per_gem | 627649.3987 |
| bc_on_whitelist | 0.9199654904 |
| bc_mean_qscore | 38.00175612 |
| n50_linked_reads_per_molecule | 7 |
| corrected_loaded_mass_ng | 1.47646699 |
| snps_phased | 0.8821166619 |
| genes_phased_lt_100kb | 0.6786503314 |
| longest_phase_block | 613790 |
| n50_phase_block | 40966 |
| molecule_length_mean | 20965.29929 |
| molecule_length_stddev | 43841.19863 |
| number_reads | 788378892 |
| median_insert_size | 271 |
| mean_depth | 35.16779187 |
| zero_coverage | 0.02479407883 |
| mapped_reads | 0.9462876563 |
| pcr_duplication | 0.03490774745 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9387863377 |
| r1_q30_bases_fract | 0.8732901139 |
| r2_q20_bases_fract | 0.8809673288 |
| r2_q30_bases_fract | 0.7850798897 |
| si_q20_bases_fract | 0.9560422918 |
| si_q30_bases_fract | 0.9218783413 |
| bc_q20_bases_fract | 0.9893101255 |
| bc_q30_bases_fract | 0.9677098448 |
| large_sv_calls | 2013 |
| short_deletion_calls | 29830 |
Deepvariant results
| index | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | 305 | 306 | 307 | 308 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.DV1 | 4512-JFI-0582.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 | 49458 | 31564 | 33569 | 49634 | 51292 | 41026 | 37989 | 44543 | 36863 | 31337 | 112975 | 30996 | 119791 | 77062 | 74155 | 84841 | 61743 | 63450 | 53292 | 52890 | 52874 | 439 |
| Biallelic_Insertion | 49785 | 32115 | 30839 | 47743 | 49206 | 40496 | 36426 | 41769 | 35606 | 29574 | 109083 | 29333 | 114473 | 74894 | 71813 | 80530 | 60472 | 61297 | 53337 | 50898 | 50934 | 591 |
| Biallelic_SNP | 176228 | 124782 | 125945 | 196334 | 238047 | 162848 | 146310 | 181073 | 145131 | 122720 | 523544 | 129362 | 631305 | 327501 | 331967 | 372624 | 247363 | 290115 | 201422 | 225770 | 139361 | 2805 |
| Multiallelic_Complex | 1542 | 799 | 931 | 1254 | 1350 | 1108 | 922 | 1129 | 911 | 863 | 3235 | 772 | 3085 | 2050 | 1838 | 2106 | 1598 | 1748 | 1506 | 1372 | 858 | 21 |
| Multiallelic_Deletion | 3296 | 1511 | 1730 | 2509 | 2572 | 1758 | 1646 | 2379 | 1924 | 1783 | 6421 | 1386 | 6460 | 4351 | 4032 | 4700 | 3195 | 3691 | 2997 | 2773 | 1637 | 29 |
| Multiallelic_Insertion | 5493 | 2543 | 3114 | 4062 | 4283 | 2855 | 2742 | 3832 | 3144 | 2777 | 10498 | 2457 | 10773 | 7270 | 6498 | 7843 | 5401 | 6238 | 4838 | 4583 | 2461 | 52 |
| Multiallelic_SNP | 107 | 60 | 168 | 82 | 160 | 168 | 102 | 145 | 67 | 208 | 513 | 114 | 492 | 251 | 198 | 198 | 207 | 217 | 146 | 204 | 97 | 1 |
| RefCall | 364540 | 249123 | 225510 | 338312 | 358191 | 327053 | 268612 | 312584 | 255576 | 240489 | 925153 | 212829 | 891361 | 560511 | 542978 | 563940 | 459134 | 474792 | 392302 | 388980 | 463253 | 28534 |
| Transition | 114285 | 77403 | 80105 | 119623 | 147654 | 96926 | 89786 | 116393 | 92058 | 76909 | 323351 | 81703 | 384152 | 205953 | 205384 | 233297 | 151281 | 183141 | 129097 | 140737 | 76583 | 1474 |
| Transversion | 61943 | 47379 | 45840 | 76711 | 90393 | 65922 | 56524 | 64680 | 53073 | 45811 | 200193 | 47659 | 247153 | 121548 | 126583 | 139327 | 96082 | 106974 | 72325 | 85033 | 62778 | 1331 |