Detailed view of 95-39689
Strain
| ID | 67 |
|---|---|
| Name | HXB24 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB24_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0534 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0534 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 29.6 |
| 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 | 95-39689 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 86 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39689.LR1 | 95-39689.SN1 | 95-39689.GH1 | 95-39689.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/HXB24 | supernova_results/HXB24 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-07 | 2020-01-26 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39689.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1886541 |
| mean_dna_per_gem | 669412.5219 |
| bc_on_whitelist | 0.9124678793 |
| bc_mean_qscore | 36.43372501 |
| n50_linked_reads_per_molecule | 15 |
| corrected_loaded_mass_ng | 1.574709533 |
| snps_phased | 0.8942380949 |
| genes_phased_lt_100kb | 0.8335269067 |
| longest_phase_block | 1604639 |
| n50_phase_block | 94400 |
| molecule_length_mean | 28043.30234 |
| molecule_length_stddev | 46660.36306 |
| number_reads | 1235149830 |
| median_insert_size | 289 |
| mean_depth | 55.07638235 |
| zero_coverage | 0.02136217784 |
| mapped_reads | 0.9367457857 |
| pcr_duplication | 0.05026715376 |
| on_target_bases | |
| r1_q20_bases_fract | 0.951259626 |
| r1_q30_bases_fract | 0.9078356462 |
| r2_q20_bases_fract | 0.9357178836 |
| r2_q30_bases_fract | 0.8840446311 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9885903967 |
| bc_q30_bases_fract | 0.9667342405 |
| large_sv_calls | 2346 |
| short_deletion_calls | 31739 |
Deepvariant results
| index | 793 | 794 | 795 | 796 | 797 | 798 | 799 | 800 | 801 | 802 | 803 | 804 | 805 | 806 | 807 | 808 | 809 | 810 | 811 | 812 | 813 | 814 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.DV1 | 95-39689.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 | 47417 | 29794 | 25211 | 34414 | 52067 | 32283 | 28576 | 33864 | 20327 | 18845 | 92267 | 19630 | 115602 | 51562 | 62406 | 73381 | 59065 | 41670 | 57865 | 54446 | 47545 | 422 |
| Biallelic_Insertion | 44437 | 28613 | 22858 | 32273 | 47245 | 30491 | 26160 | 31042 | 20120 | 17820 | 86030 | 18559 | 105678 | 49228 | 57927 | 66434 | 54555 | 40608 | 52509 | 49105 | 45144 | 558 |
| Biallelic_SNP | 164177 | 117991 | 64491 | 68340 | 240820 | 95774 | 69434 | 100337 | 19838 | 33941 | 365397 | 31880 | 582989 | 142034 | 228673 | 270221 | 223359 | 135345 | 236415 | 234130 | 105432 | 2750 |
| Multiallelic_Complex | 1270 | 640 | 545 | 723 | 1077 | 745 | 585 | 788 | 402 | 444 | 2326 | 385 | 2434 | 1245 | 1378 | 1577 | 1302 | 1183 | 1405 | 1225 | 808 | 11 |
| Multiallelic_Deletion | 2577 | 1024 | 641 | 960 | 2119 | 800 | 638 | 943 | 315 | 268 | 3403 | 288 | 4730 | 1399 | 2322 | 2874 | 2241 | 1258 | 2734 | 2253 | 1133 | 36 |
| Multiallelic_Insertion | 4780 | 1957 | 1420 | 1703 | 3945 | 1472 | 1258 | 1920 | 674 | 641 | 6299 | 763 | 8959 | 2716 | 4396 | 5345 | 4336 | 2379 | 5083 | 4207 | 2055 | 56 |
| Multiallelic_SNP | 110 | 60 | 65 | 48 | 140 | 110 | 72 | 93 | 27 | 90 | 351 | 21 | 361 | 131 | 84 | 117 | 142 | 142 | 120 | 204 | 63 | 27689 |
| RefCall | 273393 | 193140 | 166434 | 232089 | 282294 | 247255 | 193697 | 225375 | 161778 | 168169 | 699449 | 132927 | 686146 | 379760 | 383536 | 402932 | 336201 | 339860 | 320170 | 316295 | 440067 | 1432 |
| Transition | 105856 | 71317 | 37985 | 39672 | 149833 | 55640 | 40085 | 60724 | 8428 | 16384 | 217264 | 16680 | 355262 | 81682 | 138264 | 167661 | 135832 | 79017 | 151087 | 145869 | 55270 | 1318 |
| Transversion | 58321 | 46674 | 26506 | 28668 | 90987 | 40134 | 29349 | 39613 | 11410 | 17557 | 148133 | 15200 | 227727 | 60352 | 90409 | 102560 | 87527 | 56328 | 85328 | 88261 | 50162 |
Supernova results
| Analysis_ID | 95-39689.SN1 |
|---|---|
| assembly_size | 2456292004 |
| barcode_fraction | 1 |
| bases_per_read | 137.44 |
| bridge_1_50 | 90.636 |
| bridge_50 | 0.022 |
| bridge_model_badness_of_fit | 1.09334 |
| checksum | -3.68668e+18 |
| contig_N50 | 34138 |
| dinucleotide_percent | 1.42495 |
| dup_perc | 16.0769 |
| edge_N50 | 7901 |
| effective_coverage | 41.7816 |
| est_genome_size | 3180000000 |
| gc_percent | 42.0484 |
| hetdist | 46095 |
| high_AT_index | 0.0729646 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 22223 |
| m10 | 2.69527 |
| median_ins_sz | 305 |
| nreads | 1235149830 |
| p10 | 41.3824 |
| phase_block_N50 | 29567 |
| placed_perc | 60.0932 |
| proper_pairs_perc | 92.4036 |
| q30_r2_perc | 88.4045 |
| raw_coverage | 57.7695 |
| read_rate_DF_1_threaded | 36.035 |
| read_rate_IO_10_threaded | 2939.04 |
| read_rate_IO_1_threaded | 3481.37 |
| repfrac | 10.7288 |
| rpb_N50 | 816 |
| scaffold_N50 | 2508661 |
| scaffolds_10kb_plus | 6625 |
| scaffolds_1kb_plus | 36349 |
| unbar_perc | 8.75321 |
| valid_bc_perc | 91.2468 |