Detailed view of 95-39671
Strain
| ID | 47 |
|---|---|
| Name | BXH11 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH11_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0516 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0516 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 35.6 |
| 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 | 95-39671 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 94 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39671.LR1 | 95-39671.SN1 | 95-39671.GH1 | 95-39671.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/BXH11 | supernova_results/BXH11 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-02 | 2020-02-09 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39671.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1749527 |
| mean_dna_per_gem | 718259.7399 |
| bc_on_whitelist | 0.9256667838 |
| bc_mean_qscore | 36.32761333 |
| n50_linked_reads_per_molecule | 20 |
| corrected_loaded_mass_ng | 1.689616526 |
| snps_phased | 0.9034881557 |
| genes_phased_lt_100kb | 0.8946040373 |
| longest_phase_block | 1896947 |
| n50_phase_block | 193725 |
| molecule_length_mean | 38916.0924 |
| molecule_length_stddev | 52685.53954 |
| number_reads | 1318783082 |
| median_insert_size | 311 |
| mean_depth | 60.96319696 |
| zero_coverage | 0.02078920137 |
| mapped_reads | 0.9557480462 |
| pcr_duplication | 0.05115813547 |
| on_target_bases | |
| r1_q20_bases_fract | 0.958350589 |
| r1_q30_bases_fract | 0.9158913014 |
| r2_q20_bases_fract | 0.9500109168 |
| r2_q30_bases_fract | 0.9005208047 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9861938531 |
| bc_q30_bases_fract | 0.9608252656 |
| large_sv_calls | 2360 |
| short_deletion_calls | 37488 |
Deepvariant results
| index | 375 | 376 | 377 | 378 | 379 | 380 | 381 | 382 | 383 | 384 | 385 | 386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 | 394 | 395 | 396 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.DV1 | 95-39671.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 | 41808 | 30936 | 35163 | 49638 | 36532 | 33520 | 27849 | 27693 | 33113 | 28002 | 110242 | 23430 | 102708 | 53263 | 75390 | 80526 | 58344 | 60056 | 38505 | 42988 | 39996 | 111 |
| Biallelic_Insertion | 39066 | 28593 | 30326 | 44619 | 33557 | 30851 | 24791 | 25358 | 30025 | 24860 | 99159 | 20812 | 93590 | 49214 | 67495 | 71746 | 53222 | 54952 | 35815 | 38800 | 37958 | 271 |
| Biallelic_SNP | 121847 | 124051 | 134537 | 205301 | 111550 | 99677 | 60553 | 51090 | 113610 | 97350 | 485126 | 64353 | 477148 | 161800 | 321467 | 328527 | 236169 | 277481 | 92191 | 134473 | 54401 | 647 |
| Multiallelic_Complex | 1058 | 591 | 776 | 959 | 700 | 703 | 510 | 534 | 573 | 590 | 2628 | 456 | 2093 | 1137 | 1511 | 1468 | 1186 | 1394 | 769 | 862 | 637 | 5 |
| Multiallelic_Deletion | 1886 | 1013 | 1503 | 1773 | 1023 | 803 | 554 | 464 | 1087 | 941 | 4558 | 618 | 3488 | 1382 | 2921 | 2789 | 1988 | 2268 | 1036 | 1294 | 521 | 5 |
| Multiallelic_Insertion | 3541 | 1951 | 2843 | 3348 | 1982 | 1456 | 1088 | 961 | 2139 | 1769 | 8335 | 1153 | 6781 | 2584 | 5576 | 5403 | 3834 | 4517 | 2161 | 2495 | 877 | 4 |
| Multiallelic_SNP | 70 | 64 | 153 | 88 | 72 | 84 | 42 | 66 | 59 | 91 | 388 | 101 | 314 | 135 | 125 | 146 | 305 | 223 | 61 | 123 | 42 | 27234 |
| RefCall | 243205 | 176041 | 183039 | 241424 | 223711 | 232267 | 177079 | 196214 | 170789 | 177499 | 687079 | 149564 | 599455 | 361162 | 372788 | 382196 | 375774 | 357901 | 254892 | 261118 | 410857 | 384 |
| Transition | 76472 | 75848 | 86073 | 119225 | 63865 | 56759 | 34078 | 27228 | 70413 | 59092 | 298394 | 38437 | 287130 | 91440 | 200254 | 202096 | 140925 | 170342 | 52633 | 80538 | 25058 | 263 |
| Transversion | 45375 | 48203 | 48464 | 86076 | 47685 | 42918 | 26475 | 23862 | 43197 | 38258 | 186732 | 25916 | 190018 | 70360 | 121213 | 126431 | 95244 | 107139 | 39558 | 53935 | 29343 |
Supernova results
| Analysis_ID | 95-39671.SN1 |
|---|---|
| assembly_size | 2541531655 |
| barcode_fraction | 1 |
| bases_per_read | 138.002 |
| bridge_1_50 | 12.738 |
| bridge_50 | 0.179 |
| bridge_model_badness_of_fit | 1.0192 |
| checksum | -3.5975e+18 |
| contig_N50 | 32958 |
| dinucleotide_percent | 1.00859 |
| dup_perc | 15.6643 |
| edge_N50 | 7704 |
| effective_coverage | 50.8594 |
| est_genome_size | 2860000000 |
| gc_percent | 42.3239 |
| hetdist | 38108 |
| high_AT_index | 0.0759578 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 38797.1 |
| m10 | 3.42772 |
| median_ins_sz | 324 |
| nreads | 1318783082 |
| p10 | 92.1176 |
| phase_block_N50 | 137095 |
| placed_perc | 59.555 |
| proper_pairs_perc | 92.4135 |
| q30_r2_perc | 90.0521 |
| raw_coverage | 68.8933 |
| read_rate_DF_1_threaded | 8.04406 |
| read_rate_IO_10_threaded | 3147.19 |
| read_rate_IO_1_threaded | 2623.18 |
| repfrac | 8.18067 |
| rpb_N50 | 868 |
| scaffold_N50 | 14254905 |
| scaffolds_10kb_plus | 12742 |
| scaffolds_1kb_plus | 51879 |
| unbar_perc | 7.43332 |
| valid_bc_perc | 92.5667 |