Detailed view of 4512-JFI-0335
Strain
| ID | 34 |
|---|---|
| Name | WLI/EER |
| Type | Inbred |
| Living | False |
| Source | Eva Redei |
| Note |
Animal
| Animal_name | WLI/Ere_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | |
| Source | Chen |
| Note |
Tissue
| ID | 4512-JFI-0175 |
|---|---|
| Type | liver |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0175 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 33.4 |
| 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: 2 |
| Raw_data_dir_name | 4512-JFI-0509 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 62 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0335.LR1 | 4512-JFI-0335.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0335_wli | /data/10_TB/deepvar |
| Analysis_date | 2019-01-04 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0335.LR1 |
|---|---|
| instrument_ids | E00247 |
| gems_detected | 1614895 |
| mean_dna_per_gem | 346665.3431 |
| bc_on_whitelist | 0.9251791115 |
| bc_mean_qscore | 38.37860168 |
| n50_linked_reads_per_molecule | 10 |
| corrected_loaded_mass_ng | 0.815487017 |
| snps_phased | 0.8646097953 |
| genes_phased_lt_100kb | 0.58294195 |
| longest_phase_block | 447938 |
| n50_phase_block | 34098 |
| molecule_length_mean | 20821.74154 |
| molecule_length_stddev | 40793.56208 |
| number_reads | 665895674 |
| median_insert_size | 311 |
| mean_depth | 29.1288948 |
| zero_coverage | 0.02790955197 |
| mapped_reads | 0.9279162279 |
| pcr_duplication | 0.04525296024 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9387007367 |
| r1_q30_bases_fract | 0.8801659018 |
| r2_q20_bases_fract | 0.8309997012 |
| r2_q30_bases_fract | 0.7050638311 |
| si_q20_bases_fract | 0.9440386554 |
| si_q30_bases_fract | 0.9114503524 |
| bc_q20_bases_fract | 0.9918755734 |
| bc_q30_bases_fract | 0.9794813063 |
| large_sv_calls | 2778 |
| short_deletion_calls | 29397 |
Deepvariant results
| index | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.DV1 | 4512-JFI-0335.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 | 54219 | 34737 | 32686 | 51622 | 54058 | 45399 | 43884 | 46494 | 34871 | 32627 | 115826 | 31653 | 117327 | 78445 | 78778 | 86962 | 68432 | 64458 | 60278 | 54522 | 50698 | 168 |
| Biallelic_Insertion | 51881 | 33619 | 29206 | 48802 | 50411 | 43496 | 40695 | 42565 | 33288 | 29599 | 108790 | 29006 | 111018 | 74290 | 73800 | 80302 | 64646 | 60892 | 56613 | 51134 | 44029 | 247 |
| Biallelic_SNP | 208059 | 149160 | 123099 | 223610 | 254283 | 197311 | 195651 | 193509 | 128277 | 129206 | 551959 | 132816 | 595611 | 339773 | 352631 | 380651 | 310341 | 304115 | 249663 | 236254 | 168068 | 964 |
| Multiallelic_Complex | 1360 | 724 | 698 | 1005 | 1106 | 966 | 884 | 1018 | 699 | 797 | 2639 | 655 | 2456 | 1638 | 1664 | 1752 | 1322 | 1504 | 1369 | 1230 | 582 | 4 |
| Multiallelic_Deletion | 2957 | 1432 | 1247 | 2217 | 2345 | 1727 | 1744 | 2078 | 1362 | 1393 | 5253 | 1176 | 5126 | 3502 | 3589 | 3836 | 3019 | 3012 | 2935 | 2251 | 996 | 4 |
| Multiallelic_Insertion | 4600 | 2195 | 1982 | 3310 | 3763 | 2715 | 2903 | 3257 | 2113 | 2182 | 7990 | 1761 | 8031 | 5580 | 5726 | 6140 | 4829 | 4681 | 4550 | 3732 | 1626 | 24177 |
| Multiallelic_SNP | 114 | 80 | 137 | 84 | 150 | 124 | 122 | 132 | 73 | 202 | 477 | 125 | 436 | 245 | 152 | 181 | 344 | 261 | 135 | 225 | 89 | 514 |
| RefCall | 475358 | 320452 | 262781 | 433555 | 443640 | 399901 | 358965 | 389763 | 307433 | 289846 | 1111154 | 258379 | 1053118 | 690133 | 685041 | 704315 | 614443 | 590096 | 521955 | 480156 | 390965 | 450 |
| Transition | 136232 | 93065 | 78380 | 132409 | 158942 | 121247 | 123295 | 124797 | 81475 | 81364 | 341329 | 84715 | 364613 | 212814 | 220432 | 238786 | 190021 | 189711 | 161152 | 147130 | 92808 | |
| Transversion | 71827 | 56095 | 44719 | 91201 | 95341 | 76064 | 72356 | 68712 | 46802 | 47842 | 210630 | 48101 | 230998 | 126959 | 132199 | 141865 | 120320 | 114404 | 88511 | 89124 | 75260 |