Detailed view of 95-39674
Strain
| ID | 56 |
|---|---|
| Name | HXB1 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB1_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0519 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0519 |
|---|---|
| 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_X |
| Sequencing_date | 2019-09-01 |
| Sequencing_facility | USUHS |
| Sequencing_notes | |
| Raw_data_dir_name | 95-39674 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 110 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39674.LR1 | 95-39674.SN1 | 95-39674.GH1 | 95-39674.DV1 |
|---|---|---|---|---|
| Software_name | LongRanger | Supernova | GROC-SVs | DeepVariant |
| Software_version | 2.2.2 | 2.1.1 | Udit_PR3 | 0.9.0-gpu |
| Results_dir | longranger_results/HXB1 | supernova_results/HXB1 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-02 | 2020-02-02 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39674.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1502247 |
| mean_dna_per_gem | 800016.2366 |
| bc_on_whitelist | 0.9282625329 |
| bc_mean_qscore | 36.44253013 |
| n50_linked_reads_per_molecule | 24 |
| corrected_loaded_mass_ng | 1.881938496 |
| snps_phased | 0.8913914002 |
| genes_phased_lt_100kb | 0.8927879023 |
| longest_phase_block | 2629336 |
| n50_phase_block | 168174 |
| molecule_length_mean | 34457.56379 |
| molecule_length_stddev | 54119.3686 |
| number_reads | 1568162866 |
| median_insert_size | 303 |
| mean_depth | 71.14842605 |
| zero_coverage | 0.02003097554 |
| mapped_reads | 0.9466403319 |
| pcr_duplication | 0.08353882923 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9564838612 |
| r1_q30_bases_fract | 0.9156640042 |
| r2_q20_bases_fract | 0.9449629832 |
| r2_q30_bases_fract | 0.8969698546 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9887453984 |
| bc_q30_bases_fract | 0.9673204213 |
| large_sv_calls | 2533 |
| short_deletion_calls | 34459 |
Deepvariant results
| index | 683 | 684 | 685 | 686 | 687 | 688 | 689 | 690 | 691 | 692 | 693 | 694 | 695 | 696 | 697 | 698 | 699 | 700 | 701 | 702 | 703 | 704 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.DV1 | 95-39674.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 | 38765 | 26635 | 25738 | 48263 | 39311 | 37820 | 30850 | 32035 | 30429 | 32277 | 100289 | 21972 | 80747 | 67422 | 62502 | 65714 | 59007 | 49726 | 42394 | 38317 | 54726 | 392 |
| Biallelic_Insertion | 36009 | 25554 | 22852 | 43531 | 35910 | 34664 | 27803 | 28900 | 27751 | 28036 | 90836 | 19781 | 74806 | 61300 | 56699 | 59029 | 53771 | 45667 | 39120 | 35379 | 50164 | 528 |
| Biallelic_SNP | 102125 | 94664 | 65449 | 199422 | 143328 | 144644 | 84929 | 81016 | 95193 | 132021 | 412622 | 46801 | 287051 | 255693 | 221843 | 217941 | 252124 | 196829 | 122214 | 120220 | 155113 | 2907 |
| Multiallelic_Complex | 1006 | 548 | 607 | 996 | 783 | 817 | 624 | 677 | 580 | 736 | 2466 | 474 | 1877 | 1489 | 1379 | 1369 | 1315 | 1350 | 985 | 799 | 1057 | 13 |
| Multiallelic_Deletion | 1723 | 741 | 724 | 1875 | 1126 | 1200 | 804 | 900 | 1031 | 1427 | 4216 | 535 | 2456 | 2565 | 2459 | 2260 | 2178 | 1979 | 1442 | 994 | 1940 | 32 |
| Multiallelic_Insertion | 3225 | 1488 | 1545 | 3384 | 2175 | 2068 | 1608 | 1757 | 1926 | 2668 | 7431 | 1134 | 4648 | 4713 | 4317 | 4137 | 4157 | 3581 | 2919 | 2003 | 3369 | 72 |
| Multiallelic_SNP | 53 | 40 | 48 | 89 | 114 | 114 | 62 | 72 | 47 | 190 | 329 | 23 | 238 | 106 | 86 | 112 | 315 | 220 | 86 | 144 | 96 | 3 |
| RefCall | 227857 | 160966 | 156109 | 230131 | 233485 | 237440 | 174919 | 192483 | 159094 | 183597 | 652771 | 124283 | 537923 | 360779 | 331200 | 342926 | 368751 | 327896 | 255388 | 256286 | 472932 | 28909 |
| Transition | 63220 | 55257 | 38877 | 114659 | 85753 | 84635 | 49198 | 48543 | 58704 | 83453 | 251359 | 27748 | 168839 | 155968 | 136360 | 130867 | 149969 | 117858 | 73784 | 68883 | 83388 | 1540 |
| Transversion | 38905 | 39407 | 26572 | 84763 | 57575 | 60009 | 35731 | 32473 | 36489 | 48568 | 161263 | 19053 | 118212 | 99725 | 85483 | 87074 | 102155 | 78971 | 48430 | 51337 | 71725 | 1367 |
Supernova results
| Analysis_ID | 95-39674.SN1 |
|---|---|
| assembly_size | 2576923616 |
| barcode_fraction | 1 |
| bases_per_read | 137.643 |
| bridge_1_50 | 21.918 |
| bridge_50 | 0.153 |
| bridge_model_badness_of_fit | 1.0126 |
| checksum | 7.711789508072858e+18 |
| contig_N50 | 30701 |
| dinucleotide_percent | 1.25155 |
| dup_perc | 18.5535 |
| edge_N50 | 7472 |
| effective_coverage | 54.9167 |
| est_genome_size | 3020000000 |
| gc_percent | 42.4514 |
| hetdist | 15778 |
| high_AT_index | 0.0731546 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 31796 |
| m10 | 4.14754 |
| median_ins_sz | 318 |
| nreads | 1568162866 |
| p10 | 65.2647 |
| phase_block_N50 | 144493 |
| placed_perc | 49.1055 |
| proper_pairs_perc | 92.305 |
| q30_r2_perc | 89.697 |
| raw_coverage | 77.4809 |
| read_rate_DF_1_threaded | 34.6983 |
| read_rate_IO_10_threaded | 3029.79 |
| read_rate_IO_1_threaded | 3225.36 |
| repfrac | 9.49942 |
| rpb_N50 | 1224 |
| scaffold_N50 | 5787906 |
| scaffolds_10kb_plus | 18011 |
| scaffolds_1kb_plus | 63279 |
| unbar_perc | 7.17375 |
| valid_bc_perc | 92.8263 |