Detailed view of 95-39673
Strain
| ID | 49 |
|---|---|
| Name | BXH13 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH13_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0518 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0518 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 24.4 |
| 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 | 95-39673 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 89 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39673.LR1 | 95-39673.SN1 | 95-39673.GH1 | 95-39673.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/BXH13 | supernova_results/BXH13 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-01 | 2020-02-23 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39673.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1511520 |
| mean_dna_per_gem | 690756.381 |
| bc_on_whitelist | 0.9281573595 |
| bc_mean_qscore | 36.45024333 |
| n50_linked_reads_per_molecule | 14 |
| corrected_loaded_mass_ng | 1.624918302 |
| snps_phased | 0.9101832542 |
| genes_phased_lt_100kb | 0.8685049709 |
| longest_phase_block | 5264710 |
| n50_phase_block | 114320 |
| molecule_length_mean | 25171.42632 |
| molecule_length_stddev | 57710.86963 |
| number_reads | 1264382342 |
| median_insert_size | 317 |
| mean_depth | 57.27270186 |
| zero_coverage | 0.02006121371 |
| mapped_reads | 0.9465844913 |
| pcr_duplication | 0.08018100047 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9561473249 |
| r1_q30_bases_fract | 0.9152415265 |
| r2_q20_bases_fract | 0.9444764653 |
| r2_q30_bases_fract | 0.8960571148 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9889564547 |
| bc_q30_bases_fract | 0.967774746 |
| large_sv_calls | 2330 |
| short_deletion_calls | 32584 |
Deepvariant results
| index | 419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 | 427 | 428 | 429 | 430 | 431 | 432 | 433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.DV1 | 95-39673.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 | 46338 | 24317 | 29735 | 42964 | 43676 | 31564 | 30507 | 25890 | 29561 | 20668 | 67983 | 20727 | 112213 | 58342 | 63782 | 68197 | 50901 | 46421 | 50668 | 49768 | 47333 | 102 |
| Biallelic_Insertion | 43286 | 23410 | 26452 | 39400 | 40149 | 29850 | 27846 | 24729 | 27439 | 19481 | 65663 | 19040 | 102651 | 54405 | 58793 | 62071 | 47959 | 43666 | 46661 | 45311 | 46486 | 314 |
| Biallelic_SNP | 152601 | 67462 | 100921 | 156872 | 172414 | 90741 | 82717 | 42041 | 87374 | 48184 | 158479 | 36391 | 559989 | 190046 | 236312 | 220813 | 177829 | 165118 | 181618 | 201192 | 104783 | 659 |
| Multiallelic_Complex | 1204 | 533 | 719 | 915 | 920 | 774 | 652 | 541 | 641 | 512 | 1837 | 423 | 2449 | 1350 | 1446 | 1809 | 1195 | 1157 | 1176 | 1158 | 853 | 8 |
| Multiallelic_Deletion | 2418 | 812 | 1093 | 1523 | 1634 | 768 | 772 | 443 | 961 | 347 | 1581 | 452 | 4571 | 2081 | 2451 | 2222 | 1590 | 1749 | 2097 | 1929 | 1333 | 5 |
| Multiallelic_Insertion | 4583 | 1478 | 2147 | 2808 | 3084 | 1403 | 1543 | 909 | 1808 | 794 | 3023 | 1020 | 8690 | 3847 | 4537 | 3835 | 2970 | 3307 | 4006 | 3743 | 2134 | 10 |
| Multiallelic_SNP | 83 | 44 | 127 | 72 | 104 | 124 | 58 | 65 | 39 | 73 | 175 | 19 | 339 | 154 | 86 | 78 | 204 | 148 | 111 | 183 | 70 | 26396 |
| RefCall | 259783 | 170329 | 175975 | 236649 | 252384 | 238110 | 187360 | 200619 | 172800 | 168126 | 608029 | 129964 | 635654 | 381067 | 364708 | 364523 | 362565 | 333152 | 286263 | 291131 | 423827 | 384 |
| Transition | 97985 | 40927 | 62468 | 87165 | 103583 | 50763 | 49047 | 21393 | 54363 | 25247 | 83397 | 20661 | 339366 | 113831 | 144084 | 136906 | 104470 | 100356 | 114925 | 124199 | 54310 | 275 |
| Transversion | 54616 | 26535 | 38453 | 69707 | 68831 | 39978 | 33670 | 20648 | 33011 | 22937 | 75082 | 15730 | 220623 | 76215 | 92228 | 83907 | 73359 | 64762 | 66693 | 76993 | 50473 |
Supernova results
| Analysis_ID | 95-39673.SN1 |
|---|---|
| assembly_size | 2459404687 |
| barcode_fraction | 1 |
| bases_per_read | 137.549 |
| bridge_1_50 | 32.654 |
| bridge_50 | 0.075 |
| bridge_model_badness_of_fit | 1.12797 |
| checksum | -4.72757e+18 |
| contig_N50 | 33780 |
| dinucleotide_percent | 1.22662 |
| dup_perc | 18.0466 |
| edge_N50 | 7340 |
| effective_coverage | 44.1765 |
| est_genome_size | 3040000000 |
| gc_percent | 42.0754 |
| hetdist | 15731 |
| high_AT_index | 0.0755752 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 28217.3 |
| m10 | 2.65513 |
| median_ins_sz | 334 |
| nreads | 1264382342 |
| p10 | 30.5 |
| phase_block_N50 | 1841807 |
| placed_perc | 61.5134 |
| proper_pairs_perc | 91.6858 |
| q30_r2_perc | 89.6057 |
| raw_coverage | 62.0347 |
| read_rate_DF_1_threaded | 19.0728 |
| read_rate_IO_10_threaded | 2518.05 |
| read_rate_IO_1_threaded | 3274.79 |
| repfrac | 9.69353 |
| rpb_N50 | 970 |
| scaffold_N50 | 6487080 |
| scaffolds_10kb_plus | 5237 |
| scaffolds_1kb_plus | 36417 |
| unbar_perc | 7.18426 |
| valid_bc_perc | 92.8157 |