Detailed view of 95-39668
Strain
| ID | 54 |
|---|---|
| Name | BXH8 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH8_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0513 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0513 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 31 |
| 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 | 95-39668 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 89 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39668.LR1 | 95-39668.SN1 | 95-39668.GH1 | 95-39668.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/BXH8 | supernova_results/BXH8 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-09-30 | 2020-03-03 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39668.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1722225 |
| mean_dna_per_gem | 753329.4376 |
| bc_on_whitelist | 0.9180114681 |
| bc_mean_qscore | 36.42606442 |
| n50_linked_reads_per_molecule | 21 |
| corrected_loaded_mass_ng | 1.772113619 |
| snps_phased | 0.8970344964 |
| genes_phased_lt_100kb | 0.8987148769 |
| longest_phase_block | 1963607 |
| n50_phase_block | 183615 |
| molecule_length_mean | 41375.92105 |
| molecule_length_stddev | 53384.95666 |
| number_reads | 1265823592 |
| median_insert_size | 338 |
| mean_depth | 58.17800801 |
| zero_coverage | 0.02029176759 |
| mapped_reads | 0.952043188 |
| pcr_duplication | 0.05316123054 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9594891572 |
| r1_q30_bases_fract | 0.9195166043 |
| r2_q20_bases_fract | 0.9480785636 |
| r2_q30_bases_fract | 0.8993183131 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9884442434 |
| bc_q30_bases_fract | 0.9663881929 |
| large_sv_calls | 2411 |
| short_deletion_calls | 35790 |
Deepvariant results
| index | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 | 542 | 543 | 544 | 545 | 546 | 547 | 548 | 549 | 550 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.DV1 | 95-39668.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 | 47466 | 18296 | 26270 | 40767 | 49350 | 27075 | 33904 | 25901 | 36829 | 31091 | 86147 | 18160 | 79760 | 62858 | 52682 | 81299 | 56280 | 44077 | 40982 | 39066 | 42631 | 100 |
| Biallelic_Insertion | 43640 | 18092 | 23392 | 36859 | 44346 | 25318 | 30718 | 24249 | 32872 | 27219 | 79132 | 16705 | 73997 | 57316 | 47992 | 72754 | 51246 | 41633 | 37819 | 35519 | 40296 | 251 |
| Biallelic_SNP | 160255 | 21208 | 69090 | 114989 | 215582 | 47595 | 112261 | 38140 | 139119 | 122848 | 299830 | 17275 | 293324 | 212294 | 134087 | 336187 | 217686 | 147528 | 105145 | 111930 | 73520 | 572 |
| Multiallelic_Complex | 1136 | 357 | 542 | 745 | 961 | 611 | 597 | 471 | 698 | 659 | 1979 | 316 | 1712 | 1319 | 1133 | 1554 | 1118 | 1057 | 923 | 785 | 683 | 7 |
| Multiallelic_Deletion | 2358 | 311 | 705 | 1302 | 1709 | 461 | 931 | 365 | 1402 | 1126 | 2783 | 210 | 2186 | 2140 | 1658 | 2752 | 1814 | 1380 | 1299 | 941 | 760 | 1 |
| Multiallelic_Insertion | 4534 | 581 | 1493 | 2322 | 3366 | 771 | 1809 | 850 | 2599 | 2223 | 5264 | 479 | 4116 | 4143 | 3026 | 5616 | 3615 | 2630 | 2525 | 1909 | 1333 | 10 |
| Multiallelic_SNP | 87 | 28 | 61 | 39 | 120 | 66 | 77 | 56 | 67 | 196 | 294 | 11 | 262 | 103 | 49 | 127 | 280 | 172 | 58 | 101 | 45 | 25937 |
| RefCall | 253260 | 146834 | 159629 | 217102 | 249599 | 218726 | 184240 | 182910 | 172066 | 182909 | 625670 | 117978 | 543804 | 357995 | 315855 | 373747 | 362038 | 316920 | 252303 | 249659 | 383573 | 325 |
| Transition | 103274 | 9582 | 41191 | 69320 | 132937 | 22885 | 66860 | 18885 | 88614 | 76385 | 176599 | 7143 | 167815 | 130999 | 80793 | 206162 | 128979 | 85585 | 64124 | 65424 | 36170 | 247 |
| Transversion | 56981 | 11626 | 27899 | 45669 | 82645 | 24710 | 45401 | 19255 | 50505 | 46463 | 123231 | 10132 | 125509 | 81295 | 53294 | 130025 | 88707 | 61943 | 41021 | 46506 | 37350 |
Supernova results
| Analysis_ID | 95-39668.SN1 |
|---|---|
| assembly_size | 2535790089 |
| barcode_fraction | 1 |
| bases_per_read | 137.84 |
| bridge_1_50 | 10.981 |
| bridge_50 | 0.198 |
| bridge_model_badness_of_fit | 1.00843 |
| checksum | 3.9907166224642156e+18 |
| contig_N50 | 33747 |
| dinucleotide_percent | 1.12082 |
| dup_perc | 15.1496 |
| edge_N50 | 8090 |
| effective_coverage | 47.9095 |
| est_genome_size | 2930000000 |
| gc_percent | 42.308 |
| hetdist | 33681 |
| high_AT_index | 0.0749301 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 40776.2 |
| m10 | 3.23431 |
| median_ins_sz | 352 |
| nreads | 1265823592 |
| p10 | 95.0588 |
| phase_block_N50 | 139877 |
| placed_perc | 60.1339 |
| proper_pairs_perc | 92.1201 |
| q30_r2_perc | 89.9318 |
| raw_coverage | 64.5486 |
| read_rate_DF_1_threaded | 25.7866 |
| read_rate_IO_10_threaded | 2312.84 |
| read_rate_IO_1_threaded | 2127.14 |
| repfrac | 8.80836 |
| rpb_N50 | 832 |
| scaffold_N50 | 13103726 |
| scaffolds_10kb_plus | 11459 |
| scaffolds_1kb_plus | 48323 |
| unbar_perc | 8.19885 |
| valid_bc_perc | 91.8011 |