Detailed view of 4512-JFI-0504
Strain
| ID | 9 |
|---|---|
| Name | F344/NCrl |
| Type | Inbred |
| Living | False |
| Source | Charles River |
| Note |
Animal
| Animal_name | F344/NCrl_Rat1 |
|---|---|
| Sex | M |
| Age | adolescent |
| Generation | |
| Euthanasia_date | 2018-02-01 |
| Source | Charles River |
| Note | UTHSC order 6492 |
Tissue
| ID | 4512-JFI-0497 |
|---|---|
| Type | spleen |
| Transfer_History | Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0497 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 42.2 |
| 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-0504 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 78 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0504.LR1 | 4512-JFI-0504.DV1 |
|---|---|---|
| Software_name | LongRanger | DeepVariant |
| Software_version | 2.2.2 | 0.9.0-gpu |
| Results_dir | longranger_results/0504_f344ncrl | /data/10_TB/deepvar |
| Analysis_date | 2018-08-09 | 2019-12-04 |
| Note |
LongRanger results
| Analysis_ID | 4512-JFI-0504.LR1 |
|---|---|
| instrument_ids | E00438 |
| gems_detected | 1612558 |
| mean_dna_per_gem | 741126.3759 |
| bc_on_whitelist | 0.9028593658 |
| bc_mean_qscore | 38.38702493 |
| n50_linked_reads_per_molecule | 14 |
| corrected_loaded_mass_ng | 1.743407438 |
| snps_phased | 0.8762984704 |
| genes_phased_lt_100kb | 0.8480914551 |
| longest_phase_block | 1707039 |
| n50_phase_block | 165883 |
| molecule_length_mean | 43179.45143 |
| molecule_length_stddev | 50241.69547 |
| number_reads | 882111330 |
| median_insert_size | 310 |
| mean_depth | 39.94347999 |
| zero_coverage | 0.02497784168 |
| mapped_reads | 0.9482093241 |
| pcr_duplication | 0.0500568487 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9515223945 |
| r1_q30_bases_fract | 0.9007315595 |
| r2_q20_bases_fract | 0.8821410603 |
| r2_q30_bases_fract | 0.7869792259 |
| si_q20_bases_fract | 0.9654815668 |
| si_q30_bases_fract | 0.9401444212 |
| bc_q20_bases_fract | 0.9927464673 |
| bc_q30_bases_fract | 0.9794033701 |
| large_sv_calls | 2002 |
| short_deletion_calls | 36233 |
Deepvariant results
| index | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.DV1 | 4512-JFI-0504.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 | 49836 | 36879 | 33411 | 49690 | 53949 | 43898 | 42010 | 46430 | 36015 | 30726 | 105224 | 31953 | 119010 | 76328 | 75990 | 85572 | 62985 | 65877 | 57376 | 47938 | 51481 | 174 |
| Biallelic_Insertion | 50033 | 36133 | 31002 | 48499 | 51720 | 43245 | 39838 | 43520 | 35233 | 29034 | 103422 | 30080 | 114051 | 74506 | 73318 | 81037 | 62184 | 63711 | 55848 | 47237 | 49487 | 358 |
| Biallelic_SNP | 178135 | 162876 | 120941 | 203881 | 252184 | 178554 | 174048 | 194713 | 132750 | 114753 | 438147 | 130774 | 597156 | 315445 | 320979 | 362543 | 262943 | 311254 | 224099 | 178284 | 145090 | 849 |
| Multiallelic_Complex | 1585 | 915 | 904 | 1188 | 1285 | 1173 | 1028 | 1188 | 915 | 965 | 3194 | 785 | 3039 | 2011 | 1945 | 2065 | 1544 | 1883 | 1551 | 1323 | 793 | 10 |
| Multiallelic_Deletion | 3262 | 2000 | 1800 | 2459 | 2864 | 2024 | 2100 | 2655 | 1880 | 1659 | 5603 | 1446 | 6536 | 4390 | 4304 | 4796 | 3163 | 3880 | 3334 | 2139 | 1440 | 4 |
| Multiallelic_Insertion | 5573 | 3515 | 3112 | 4197 | 5032 | 3478 | 3523 | 4461 | 3149 | 2669 | 9540 | 2559 | 11166 | 7418 | 7258 | 8131 | 5600 | 6839 | 5851 | 3744 | 2334 | 7 |
| Multiallelic_SNP | 101 | 76 | 159 | 86 | 135 | 158 | 110 | 167 | 76 | 233 | 416 | 154 | 412 | 212 | 146 | 176 | 322 | 234 | 137 | 190 | 110 | 2 |
| RefCall | 332712 | 243401 | 213086 | 305606 | 325855 | 309288 | 257273 | 284820 | 229348 | 221027 | 813259 | 195222 | 785695 | 511527 | 485800 | 502832 | 446567 | 439436 | 369590 | 339074 | 398150 | 27398 |
| Transition | 114984 | 102569 | 76699 | 119096 | 157864 | 107674 | 109386 | 125148 | 84810 | 72332 | 267952 | 83395 | 365843 | 197100 | 200759 | 226156 | 159458 | 197018 | 143558 | 108012 | 79367 | 472 |
| Transversion | 63151 | 60307 | 44242 | 84785 | 94320 | 70880 | 64662 | 69565 | 47940 | 42421 | 170195 | 47379 | 231313 | 118345 | 120220 | 136387 | 103485 | 114236 | 80541 | 70272 | 65723 | 377 |