Detailed view of 95-39691
Strain
| ID | 69 |
|---|---|
| Name | HXB27 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB27_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0536 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0536 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 37.4 |
| 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 | 95-39691 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 35 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39691.LR1 | 95-39691.SN1 | 95-39691.GH1 | 95-39691.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/HXB27 | supernova_results/HXB27 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-06 | 2020-01-22 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39691.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1815712 |
| mean_dna_per_gem | 585841.2128 |
| bc_on_whitelist | 0.90816507 |
| bc_mean_qscore | 36.41103486 |
| n50_linked_reads_per_molecule | 6 |
| corrected_loaded_mass_ng | 1.378118444 |
| snps_phased | 0.8648657753 |
| genes_phased_lt_100kb | 0.7105203363 |
| longest_phase_block | 784392 |
| n50_phase_block | 68636 |
| molecule_length_mean | 23772.65072 |
| molecule_length_stddev | 36257.96529 |
| number_reads | 493960000 |
| median_insert_size | 320 |
| mean_depth | 21.71887193 |
| zero_coverage | 0.02475056489 |
| mapped_reads | 0.9275177828 |
| pcr_duplication | 0.02724942756 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9457377276 |
| r1_q30_bases_fract | 0.8998085587 |
| r2_q20_bases_fract | 0.9264294472 |
| r2_q30_bases_fract | 0.8706050061 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9881428542 |
| bc_q30_bases_fract | 0.9653620556 |
| large_sv_calls | 1867 |
| short_deletion_calls | 24942 |
Deepvariant results
| index | 837 | 838 | 839 | 840 | 841 | 842 | 843 | 844 | 845 | 846 | 847 | 848 | 849 | 850 | 851 | 852 | 853 | 854 | 855 | 856 | 857 | 858 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.DV1 | 95-39691.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 | 45739 | 18883 | 23126 | 30143 | 30454 | 38324 | 28102 | 38198 | 36246 | 25240 | 66865 | 25634 | 61085 | 45115 | 65900 | 55415 | 53675 | 43258 | 33327 | 42599 | 44508 | 409 |
| Biallelic_Insertion | 46069 | 21101 | 22384 | 31190 | 31563 | 38177 | 27985 | 36228 | 35148 | 24208 | 70895 | 24902 | 65409 | 47954 | 64527 | 55299 | 53508 | 44688 | 35506 | 41851 | 39784 | 465 |
| Biallelic_SNP | 144089 | 22210 | 50580 | 34969 | 61880 | 138929 | 61911 | 125199 | 136921 | 78015 | 147330 | 80071 | 113900 | 84754 | 242250 | 112431 | 190869 | 146750 | 49222 | 131999 | 131488 | 2544 |
| Multiallelic_Complex | 996 | 397 | 461 | 533 | 643 | 743 | 544 | 759 | 711 | 515 | 1599 | 457 | 1286 | 928 | 1247 | 1045 | 1066 | 1095 | 721 | 908 | 470 | 6 |
| Multiallelic_Deletion | 2132 | 232 | 388 | 404 | 461 | 954 | 503 | 1122 | 1305 | 644 | 1125 | 613 | 877 | 624 | 2389 | 1418 | 1571 | 1039 | 534 | 1195 | 667 | 18 |
| Multiallelic_Insertion | 3544 | 362 | 806 | 672 | 838 | 1664 | 934 | 2071 | 2158 | 1151 | 2037 | 1169 | 1532 | 1124 | 3797 | 2204 | 2731 | 1873 | 974 | 2144 | 1081 | 31 |
| Multiallelic_SNP | 78 | 26 | 40 | 23 | 47 | 78 | 49 | 90 | 49 | 129 | 150 | 27 | 159 | 79 | 82 | 67 | 269 | 183 | 43 | 112 | 67 | 20456 |
| RefCall | 334938 | 183927 | 174906 | 243715 | 248424 | 279197 | 213235 | 267575 | 229806 | 192847 | 671358 | 166888 | 577307 | 401728 | 448969 | 409829 | 424336 | 377871 | 297874 | 317475 | 256054 | 1338 |
| Transition | 92822 | 10260 | 28687 | 16580 | 33874 | 80841 | 35430 | 79299 | 87207 | 46706 | 78104 | 49152 | 57790 | 43447 | 149383 | 66820 | 112322 | 83815 | 25155 | 79970 | 70771 | 1206 |
| Transversion | 51267 | 11950 | 21893 | 18389 | 28006 | 58088 | 26481 | 45900 | 49714 | 31309 | 69226 | 30919 | 56110 | 41307 | 92867 | 45611 | 78547 | 62935 | 24067 | 52029 | 60717 |
Supernova results
| Analysis_ID | 95-39691.SN1 |
|---|---|
| assembly_size | |
| barcode_fraction | |
| bases_per_read | |
| bridge_1_50 | |
| bridge_50 | |
| bridge_model_badness_of_fit | |
| checksum | |
| contig_N50 | |
| dinucleotide_percent | |
| dup_perc | |
| edge_N50 | |
| effective_coverage | |
| est_genome_size | |
| gc_percent | |
| hetdist | |
| high_AT_index | |
| likely_sequencers | |
| lw_mean_mol_len | |
| m10 | |
| median_ins_sz | |
| nreads | |
| p10 | |
| phase_block_N50 | |
| placed_perc | |
| proper_pairs_perc | |
| q30_r2_perc | |
| raw_coverage | |
| read_rate_DF_1_threaded | |
| read_rate_IO_10_threaded | |
| read_rate_IO_1_threaded | |
| repfrac | |
| rpb_N50 | |
| scaffold_N50 | |
| scaffolds_10kb_plus | |
| scaffolds_1kb_plus | |
| unbar_perc | |
| valid_bc_perc |