Detailed view of 4512-JFI-0336
Strain
| ID | 35 |
|---|---|
| Name | WMI/EER |
| Type | Inbred |
| Living | False |
| Source | Eva Redei |
| Note |
Animal
| Animal_name | WMI/Ere_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | |
| Source | Chen |
| Note |
Tissue
| ID | 4512-JFI-0176 |
|---|---|
| Type | liver |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0176 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 23.8 |
| DNA_target_length | |
| DNA_extraction_facility | HudsonAlpha |
| Library_kit | 150bp_PE |
| Library_facility | HudsonAlpha |
| Sequencing_instrument | HiSeq_X10 |
| Sequencing_date | 2017-01-21 |
| Sequencing_facility | HudsonAlpha |
| Sequencing_notes | Lanes per sample: 3 |
| Raw_data_dir_name | 4512-JFI-0510 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 76 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0336.LR1 | 4512-JFI-0336.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0336_wmi | /data/10_TB/deepvar |
| Analysis_date | 2019-01-03 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0336.LR1 |
|---|---|
| instrument_ids | E00247 |
| gems_detected | 1616286 |
| mean_dna_per_gem | 507938.294 |
| bc_on_whitelist | 0.933905956 |
| bc_mean_qscore | 38.1212661 |
| n50_linked_reads_per_molecule | 13 |
| corrected_loaded_mass_ng | 1.194861535 |
| snps_phased | 0.8843371409 |
| genes_phased_lt_100kb | 0.7580299786 |
| longest_phase_block | 782875 |
| n50_phase_block | 63557 |
| molecule_length_mean | 26886.30485 |
| molecule_length_stddev | 44500.14092 |
| number_reads | 789692638 |
| median_insert_size | 315 |
| mean_depth | 35.17316447 |
| zero_coverage | 0.0256506247 |
| mapped_reads | 0.9366066472 |
| pcr_duplication | 0.05123411834 |
| on_target_bases | |
| r1_q20_bases_fract | 0.941053015 |
| r1_q30_bases_fract | 0.8801196614 |
| r2_q20_bases_fract | 0.8282561071 |
| r2_q30_bases_fract | 0.6961795971 |
| si_q20_bases_fract | 0.9432707172 |
| si_q30_bases_fract | 0.9056046525 |
| bc_q20_bases_fract | 0.990291521 |
| bc_q30_bases_fract | 0.9719820205 |
| large_sv_calls | 2712 |
| short_deletion_calls | 35475 |
Deepvariant results
| index | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.DV1 | 4512-JFI-0336.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 | 53874 | 34494 | 33233 | 51608 | 54309 | 45341 | 43993 | 46608 | 34609 | 32422 | 116269 | 31773 | 117576 | 78188 | 78605 | 87171 | 68539 | 64229 | 60098 | 54251 | 54103 | 160 |
| Biallelic_Insertion | 50373 | 32344 | 29503 | 47790 | 49383 | 42185 | 39905 | 41891 | 32241 | 28830 | 106896 | 28749 | 108419 | 72267 | 72003 | 79273 | 63130 | 59361 | 55187 | 49865 | 48205 | 252 |
| Biallelic_SNP | 208264 | 149474 | 126410 | 224929 | 257948 | 200156 | 197492 | 194879 | 127990 | 129410 | 561680 | 133596 | 602562 | 341085 | 358131 | 382495 | 312036 | 306766 | 250554 | 236510 | 170445 | 901 |
| Multiallelic_Complex | 1376 | 723 | 761 | 1039 | 1136 | 926 | 911 | 1003 | 688 | 802 | 2770 | 635 | 2488 | 1640 | 1716 | 1698 | 1369 | 1609 | 1449 | 1302 | 743 | 3 |
| Multiallelic_Deletion | 3105 | 1433 | 1405 | 2268 | 2334 | 1721 | 1836 | 2077 | 1371 | 1571 | 5345 | 1229 | 5094 | 3621 | 3649 | 4090 | 2999 | 3150 | 3021 | 2439 | 1520 | 3 |
| Multiallelic_Insertion | 5019 | 2367 | 2396 | 3637 | 4026 | 2919 | 2958 | 3509 | 2332 | 2408 | 8708 | 1994 | 8606 | 5993 | 5990 | 6574 | 5124 | 5100 | 4880 | 3826 | 2295 | 7 |
| Multiallelic_SNP | 115 | 77 | 157 | 96 | 138 | 151 | 136 | 162 | 51 | 200 | 507 | 113 | 416 | 200 | 132 | 161 | 311 | 267 | 139 | 213 | 123 | 28245 |
| RefCall | 422327 | 278642 | 252768 | 383848 | 394616 | 356210 | 317376 | 348560 | 266882 | 264839 | 1010767 | 236242 | 941394 | 613324 | 601095 | 631156 | 548530 | 532978 | 456401 | 426682 | 536803 | 533 |
| Transition | 136333 | 93492 | 80316 | 133201 | 160804 | 122910 | 124350 | 125722 | 81370 | 81441 | 347519 | 85224 | 368943 | 213891 | 224087 | 240059 | 191198 | 191414 | 161967 | 147642 | 94500 | 368 |
| Transversion | 71931 | 55982 | 46094 | 91728 | 97144 | 77246 | 73142 | 69157 | 46620 | 47969 | 214161 | 48372 | 233619 | 127194 | 134044 | 142436 | 120838 | 115352 | 88587 | 88868 | 75945 |