Detailed view of 4512-JFI-0508
Strain
| ID | 16 |
|---|---|
| Name | LEW/SsNHsd |
| Type | Inbred |
| Living | False |
| Source | Envigo |
| Note |
Animal
| Animal_name | LEW/SsNHsd_Rat1 |
|---|---|
| Sex | M |
| Age | adolescent |
| Generation | |
| Euthanasia_date | 2018-02-01 |
| Source | Envigo |
| Note | UTHSC order 6489, foundation stock |
Tissue
| ID | 4512-JFI-0501 |
|---|---|
| Type | spleen |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0501 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 47 |
| 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-0508 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 78 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0508.LR1 | 4512-JFI-0508.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0508_lewssnhsd | /data/10_TB/deepvar |
| Analysis_date | 2018-08-08 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0508.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1570629 |
| mean_dna_per_gem | 485313.0739 |
| bc_on_whitelist | 0.8972867992 |
| bc_mean_qscore | 38.38699649 |
| n50_linked_reads_per_molecule | 12 |
| corrected_loaded_mass_ng | 1.141638525 |
| snps_phased | 0.8798655896 |
| genes_phased_lt_100kb | 0.735 |
| longest_phase_block | 553440 |
| n50_phase_block | 51839 |
| molecule_length_mean | 24942.34891 |
| molecule_length_stddev | 41126.5233 |
| number_reads | 863463482 |
| median_insert_size | 336 |
| mean_depth | 37.73594046 |
| zero_coverage | 0.02518567755 |
| mapped_reads | 0.9282834106 |
| pcr_duplication | 0.05548531515 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9382990324 |
| r1_q30_bases_fract | 0.8780083054 |
| r2_q20_bases_fract | 0.8460678633 |
| r2_q30_bases_fract | 0.7323306717 |
| si_q20_bases_fract | 0.9652593354 |
| si_q30_bases_fract | 0.9403095975 |
| bc_q20_bases_fract | 0.9926969278 |
| bc_q30_bases_fract | 0.9793696081 |
| large_sv_calls | 2361 |
| short_deletion_calls | 32220 |
Deepvariant results
| index | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 207 | 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.DV1 | 4512-JFI-0508.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 | 51063 | 29181 | 33625 | 38165 | 50543 | 40453 | 32813 | 45378 | 30923 | 27583 | 97321 | 29972 | 114944 | 76367 | 72523 | 82904 | 63043 | 59583 | 53743 | 46162 | 43465 | 156 |
| Biallelic_Insertion | 51638 | 30786 | 31049 | 39469 | 49229 | 40904 | 32748 | 43185 | 31717 | 26934 | 99464 | 28887 | 112372 | 75228 | 71927 | 80263 | 62766 | 58822 | 53609 | 46337 | 42578 | 306 |
| Biallelic_SNP | 182417 | 102150 | 124144 | 91737 | 226551 | 150124 | 97061 | 187469 | 93200 | 92769 | 393653 | 118274 | 569189 | 314603 | 297359 | 347805 | 266627 | 255726 | 197917 | 167115 | 106589 | 782 |
| Multiallelic_Complex | 1547 | 789 | 875 | 1004 | 1347 | 1055 | 857 | 1147 | 835 | 822 | 2857 | 753 | 2874 | 2026 | 1871 | 1974 | 1594 | 1731 | 1458 | 1286 | 591 | 9 |
| Multiallelic_Deletion | 3455 | 1297 | 1722 | 1416 | 2487 | 1572 | 1186 | 2428 | 1328 | 1298 | 4596 | 1211 | 6022 | 4102 | 3882 | 4264 | 3046 | 3307 | 2823 | 2054 | 791 | 9 |
| Multiallelic_Insertion | 5881 | 2193 | 3042 | 2150 | 4311 | 2746 | 1975 | 4173 | 2222 | 2145 | 7808 | 2122 | 10298 | 7141 | 6425 | 7415 | 5599 | 5666 | 4871 | 3500 | 1301 | 8 |
| Multiallelic_SNP | 109 | 59 | 156 | 35 | 118 | 128 | 73 | 146 | 47 | 230 | 386 | 138 | 485 | 194 | 129 | 144 | 315 | 203 | 130 | 199 | 87 | 1 |
| RefCall | 339593 | 223638 | 216079 | 277012 | 322653 | 289859 | 230238 | 291997 | 215540 | 206314 | 798537 | 193387 | 785946 | 508139 | 478671 | 498802 | 450260 | 426155 | 365968 | 338564 | 344324 | 23486 |
| Transition | 118447 | 62783 | 79370 | 52465 | 140632 | 89391 | 58476 | 120510 | 57751 | 56806 | 237699 | 74386 | 348574 | 196666 | 184346 | 216427 | 160911 | 160091 | 126412 | 100670 | 56491 | 450 |
| Transversion | 63970 | 39367 | 44774 | 39272 | 85919 | 60733 | 38585 | 66959 | 35449 | 35963 | 155954 | 43888 | 220615 | 117937 | 113013 | 131378 | 105716 | 95635 | 71505 | 66445 | 50098 | 332 |