Detailed view of 95-39690
Strain
| ID | 68 |
|---|---|
| Name | HXB25 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB25_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0535 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0535 |
|---|---|
| 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 | 95-39690 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 72 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39690.LR1 | 95-39690.SN1 | 95-39690.GH1 | 95-39690.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/HXB25 | supernova_results/HXB25 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-11 | 2020-01-26 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39690.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 2011321 |
| mean_dna_per_gem | 639684.8945 |
| bc_on_whitelist | 0.9087712101 |
| bc_mean_qscore | 36.41927702 |
| n50_linked_reads_per_molecule | 7 |
| corrected_loaded_mass_ng | 1.504778994 |
| snps_phased | 0.8851007445 |
| genes_phased_lt_100kb | 0.7634884132 |
| longest_phase_block | 845128 |
| n50_phase_block | 69935 |
| molecule_length_mean | 18980.18525 |
| molecule_length_stddev | 52492.35374 |
| number_reads | 1030814550 |
| median_insert_size | 292 |
| mean_depth | 44.91940133 |
| zero_coverage | 0.02078328899 |
| mapped_reads | 0.9248300036 |
| pcr_duplication | 0.04811262228 |
| on_target_bases | |
| r1_q20_bases_fract | 0.944863588 |
| r1_q30_bases_fract | 0.8985356705 |
| r2_q20_bases_fract | 0.9245348239 |
| r2_q30_bases_fract | 0.8680926422 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9882869586 |
| bc_q30_bases_fract | 0.9658917084 |
| large_sv_calls | 1912 |
| short_deletion_calls | 29095 |
Deepvariant results
| index | 815 | 816 | 817 | 818 | 819 | 820 | 821 | 822 | 823 | 824 | 825 | 826 | 827 | 828 | 829 | 830 | 831 | 832 | 833 | 834 | 835 | 836 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.DV1 | 95-39690.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 | 44189 | 21636 | 29302 | 36759 | 35696 | 37350 | 29766 | 24690 | 38049 | 23063 | 96062 | 22722 | 87054 | 57350 | 73624 | 77808 | 49872 | 44455 | 47136 | 54207 | 55020 | 418 |
| Biallelic_Insertion | 43976 | 22303 | 26868 | 35605 | 34765 | 36204 | 28586 | 24947 | 35419 | 22184 | 92229 | 22157 | 84266 | 56353 | 69237 | 72198 | 48278 | 44551 | 45433 | 50308 | 52263 | 557 |
| Biallelic_SNP | 144406 | 46411 | 99808 | 111633 | 109316 | 134343 | 78244 | 32375 | 155116 | 69697 | 396734 | 57586 | 339944 | 189269 | 320330 | 303997 | 167712 | 153439 | 151850 | 234191 | 165820 | 2844 |
| Multiallelic_Complex | 1262 | 507 | 726 | 804 | 806 | 935 | 655 | 650 | 896 | 589 | 2578 | 487 | 2147 | 1495 | 1756 | 1756 | 1274 | 1229 | 1173 | 1361 | 885 | 26 |
| Multiallelic_Deletion | 2269 | 583 | 1104 | 1077 | 1027 | 1185 | 779 | 339 | 1641 | 541 | 3883 | 595 | 3130 | 2107 | 3415 | 3377 | 1662 | 1569 | 2040 | 2371 | 1772 | 24 |
| Multiallelic_Insertion | 4277 | 1079 | 2151 | 1888 | 2007 | 2034 | 1481 | 798 | 2997 | 1204 | 6948 | 1221 | 5638 | 3781 | 6011 | 6109 | 3120 | 3033 | 3740 | 4324 | 2908 | 61 |
| Multiallelic_SNP | 73 | 34 | 104 | 52 | 76 | 108 | 52 | 65 | 76 | 128 | 364 | 35 | 268 | 151 | 132 | 142 | 261 | 139 | 83 | 195 | 103 | 26878 |
| RefCall | 321555 | 197692 | 202129 | 273302 | 280748 | 294731 | 221605 | 229927 | 238382 | 199431 | 800515 | 159858 | 694333 | 461145 | 479249 | 485736 | 415038 | 393759 | 348514 | 362194 | 462701 | 1498 |
| Transition | 92331 | 27155 | 62107 | 57695 | 62046 | 80066 | 46455 | 14640 | 99169 | 39581 | 239357 | 34588 | 203263 | 114041 | 199645 | 188847 | 98362 | 92767 | 96450 | 146312 | 90126 | 1346 |
| Transversion | 52075 | 19256 | 37701 | 53938 | 47270 | 54277 | 31789 | 17735 | 55947 | 30116 | 157377 | 22998 | 136681 | 75228 | 120685 | 115150 | 69350 | 60672 | 55400 | 87879 | 75694 |
Supernova results
| Analysis_ID | 95-39690.SN1 |
|---|---|
| assembly_size | 2416176419 |
| barcode_fraction | 1 |
| bases_per_read | 136.988 |
| bridge_1_50 | 82.027 |
| bridge_50 | 0.015 |
| bridge_model_badness_of_fit | 1.15859 |
| checksum | -7.91793e+18 |
| contig_N50 | 34992 |
| dinucleotide_percent | 1.49791 |
| dup_perc | 16.5686 |
| edge_N50 | 9592 |
| effective_coverage | 31.8472 |
| est_genome_size | 3410000000 |
| gc_percent | 41.974 |
| hetdist | 57810 |
| high_AT_index | 0.0752263 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 19141.8 |
| m10 | 3.13354 |
| median_ins_sz | 314 |
| nreads | 1030814550 |
| p10 | 13.7353 |
| phase_block_N50 | 23510 |
| placed_perc | 56.6582 |
| proper_pairs_perc | 91.9309 |
| q30_r2_perc | 86.8093 |
| raw_coverage | 44.9269 |
| read_rate_DF_1_threaded | 19.5276 |
| read_rate_IO_10_threaded | 2607.07 |
| read_rate_IO_1_threaded | 2340.04 |
| repfrac | 12.6076 |
| rpb_N50 | 706 |
| scaffold_N50 | 834712 |
| scaffolds_10kb_plus | 11204 |
| scaffolds_1kb_plus | 40294 |
| unbar_perc | 9.11608 |
| valid_bc_perc | 90.8839 |