Detailed view of 95-39679
Strain
| ID | 75 |
|---|---|
| Name | HXB7 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB7_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0524 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0524 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 28.6 |
| 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 | 95-39679 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 150 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39679.LR1 | 95-39679.SN1 | 95-39679.GH1 | 95-39679.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/HXB7 | supernova_results/HXB7 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-13 | 2020-02-14 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39679.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1592275 |
| mean_dna_per_gem | 774906.0916 |
| bc_on_whitelist | 0.9318100821 |
| bc_mean_qscore | 36.33059148 |
| n50_linked_reads_per_molecule | 33 |
| corrected_loaded_mass_ng | 1.822870009 |
| snps_phased | 0.8955744357 |
| genes_phased_lt_100kb | 0.8741030659 |
| longest_phase_block | 1643121 |
| n50_phase_block | 124916 |
| molecule_length_mean | 37215.33797 |
| molecule_length_stddev | 61272.44835 |
| number_reads | 2095290248 |
| median_insert_size | 333 |
| mean_depth | 96.22516468 |
| zero_coverage | 0.01931818974 |
| mapped_reads | 0.951952166 |
| pcr_duplication | 0.1090738469 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9559685266 |
| r1_q30_bases_fract | 0.9123679819 |
| r2_q20_bases_fract | 0.943823236 |
| r2_q30_bases_fract | 0.8909955863 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863611324 |
| bc_q30_bases_fract | 0.9607689091 |
| large_sv_calls | 2637 |
| short_deletion_calls | 34866 |
Deepvariant results
| index | 991 | 992 | 993 | 994 | 995 | 996 | 997 | 998 | 999 | 1000 | 1001 | 1002 | 1003 | 1004 | 1005 | 1006 | 1007 | 1008 | 1009 | 1010 | 1011 | 1012 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.DV1 | 95-39679.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 | 47838 | 24721 | 20788 | 35021 | 45145 | 30069 | 34293 | 36180 | 36190 | 28517 | 92846 | 18022 | 88401 | 53249 | 50964 | 71936 | 52297 | 51144 | 41650 | 32469 | 44964 | 377 |
| Biallelic_Insertion | 43719 | 23303 | 18370 | 31267 | 40393 | 27314 | 30199 | 31686 | 32034 | 24921 | 83344 | 16182 | 80074 | 47890 | 45957 | 64329 | 46874 | 46642 | 37774 | 29148 | 40023 | 493 |
| Biallelic_SNP | 174852 | 78412 | 32357 | 77532 | 181118 | 72274 | 114563 | 112028 | 136038 | 101323 | 364840 | 17856 | 365984 | 146777 | 127109 | 274580 | 177880 | 206264 | 122936 | 62492 | 84981 | 2848 |
| Multiallelic_Complex | 1093 | 423 | 375 | 536 | 849 | 678 | 597 | 691 | 615 | 591 | 2087 | 291 | 1754 | 1045 | 959 | 1264 | 987 | 1109 | 842 | 596 | 732 | 25 |
| Multiallelic_Deletion | 2538 | 633 | 216 | 945 | 1715 | 727 | 1126 | 1140 | 1427 | 1070 | 3592 | 222 | 2932 | 1596 | 1532 | 2448 | 1700 | 1921 | 1326 | 628 | 1076 | 33 |
| Multiallelic_Insertion | 4449 | 1132 | 596 | 1507 | 3007 | 1130 | 1943 | 2218 | 2492 | 1936 | 6209 | 484 | 5273 | 2759 | 2545 | 4467 | 3064 | 3409 | 2514 | 1113 | 1753 | 45 |
| Multiallelic_SNP | 64 | 32 | 49 | 54 | 105 | 72 | 85 | 74 | 61 | 116 | 354 | 15 | 317 | 87 | 58 | 121 | 130 | 161 | 71 | 102 | 75 | 2 |
| RefCall | 223517 | 143492 | 142925 | 190517 | 217908 | 212437 | 170272 | 185769 | 154945 | 168042 | 612495 | 109414 | 523815 | 310290 | 282208 | 324750 | 270575 | 305794 | 237595 | 222865 | 382297 | 26575 |
| Transition | 112968 | 45034 | 15152 | 43148 | 110877 | 39007 | 70464 | 70898 | 86398 | 62943 | 215704 | 7449 | 215468 | 85402 | 73878 | 166214 | 105725 | 124823 | 72392 | 32663 | 43038 | 1507 |
| Transversion | 61884 | 33378 | 17205 | 34384 | 70241 | 33267 | 44099 | 41130 | 49640 | 38380 | 149136 | 10407 | 150516 | 61375 | 53231 | 108366 | 72155 | 81441 | 50544 | 29829 | 41943 | 1341 |
Supernova results
| Analysis_ID | 95-39679.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 |