Detailed view of 4512-JFI-0506
Strain
| ID | 10 |
|---|---|
| Name | F344/NHsd |
| Type | Inbred |
| Living | False |
| Source | Envigo |
| Note |
Animal
| Animal_name | F344/NHsd_Rat1 |
|---|---|
| Sex | M |
| Age | adolescent |
| Generation | |
| Euthanasia_date | 2018-02-01 |
| Source | Envigo |
| Note | UTHSC order 6491, foundation stock |
Tissue
| ID | 4512-JFI-0499 |
|---|---|
| Type | spleen |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0499 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 62.8 |
| 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-0506 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 75 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0506.LR1 | 4512-JFI-0506.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0506_f344nhsd | /data/10_TB/deepvar |
| Analysis_date | 2018-08-07 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0506.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1529109 |
| mean_dna_per_gem | 611751.8654 |
| bc_on_whitelist | 0.8591841644 |
| bc_mean_qscore | 38.42979635 |
| n50_linked_reads_per_molecule | 9 |
| corrected_loaded_mass_ng | 1.439070025 |
| snps_phased | 0.869223971 |
| genes_phased_lt_100kb | 0.7109217313 |
| longest_phase_block | 532529 |
| n50_phase_block | 46229 |
| molecule_length_mean | 25755.96485 |
| molecule_length_stddev | 41150.83578 |
| number_reads | 815667354 |
| median_insert_size | 329 |
| mean_depth | 34.72461418 |
| zero_coverage | 0.02607743548 |
| mapped_reads | 0.9140942645 |
| pcr_duplication | 0.03945994316 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9246434974 |
| r1_q30_bases_fract | 0.8520002895 |
| r2_q20_bases_fract | 0.8117106229 |
| r2_q30_bases_fract | 0.6822898412 |
| si_q20_bases_fract | 0.9631410233 |
| si_q30_bases_fract | 0.9375615366 |
| bc_q20_bases_fract | 0.9930208522 |
| bc_q30_bases_fract | 0.9806546775 |
| large_sv_calls | 1919 |
| short_deletion_calls | 32718 |
Deepvariant results
| index | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.DV1 | 4512-JFI-0506.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 | 49158 | 36108 | 32778 | 48658 | 53131 | 42882 | 41424 | 46032 | 35563 | 30132 | 102480 | 31425 | 117086 | 75473 | 74613 | 83945 | 62117 | 65152 | 56669 | 46978 | 45229 | 136 |
| Biallelic_Insertion | 49586 | 35760 | 30401 | 47886 | 51308 | 42908 | 39558 | 43371 | 35224 | 28695 | 102210 | 29885 | 113614 | 74654 | 73059 | 80425 | 61747 | 63475 | 55704 | 47045 | 42097 | 238 |
| Biallelic_SNP | 175150 | 160088 | 117295 | 200707 | 247047 | 174467 | 170785 | 191690 | 131098 | 112356 | 427195 | 129139 | 585450 | 311124 | 314859 | 357228 | 259714 | 304792 | 221040 | 175757 | 135659 | 830 |
| Multiallelic_Complex | 1476 | 798 | 834 | 1071 | 1195 | 956 | 943 | 1049 | 790 | 789 | 2784 | 685 | 2667 | 1824 | 1631 | 1874 | 1372 | 1578 | 1413 | 1232 | 522 | 4 |
| Multiallelic_Deletion | 2872 | 1656 | 1593 | 2054 | 2354 | 1688 | 1725 | 2182 | 1533 | 1384 | 4751 | 1224 | 5287 | 3661 | 3568 | 4037 | 2687 | 3267 | 2826 | 1850 | 876 | 3 |
| Multiallelic_Insertion | 4632 | 2833 | 2614 | 3354 | 4081 | 2852 | 2871 | 3763 | 2528 | 2260 | 7775 | 2209 | 8895 | 6169 | 5762 | 6763 | 4615 | 5650 | 4773 | 3048 | 1390 | 3 |
| Multiallelic_SNP | 94 | 67 | 163 | 75 | 140 | 148 | 84 | 148 | 73 | 207 | 382 | 144 | 400 | 211 | 123 | 151 | 333 | 231 | 121 | 186 | 94 | 21001 |
| RefCall | 344880 | 249371 | 215960 | 317900 | 336473 | 310187 | 265539 | 295921 | 238439 | 228530 | 824635 | 199430 | 795477 | 525244 | 498705 | 514452 | 457271 | 447584 | 383755 | 347638 | 306053 | 478 |
| Transition | 113442 | 101069 | 74750 | 117492 | 155148 | 105715 | 107855 | 123365 | 83988 | 70982 | 262438 | 82568 | 359427 | 195022 | 197460 | 223410 | 158002 | 193595 | 142111 | 106838 | 74668 | 352 |
| Transversion | 61708 | 59019 | 42545 | 83215 | 91899 | 68752 | 62930 | 68325 | 47110 | 41374 | 164757 | 46571 | 226023 | 116102 | 117399 | 133818 | 101712 | 111197 | 78929 | 68919 | 60991 |