Detailed view of 95-39683
Strain
| ID | 60 |
|---|---|
| Name | HXB17 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB17_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0528 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0528 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 33.4 |
| 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 | 95-39683 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 94 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39683.LR1 | 95-39683.SN1 | 95-39683.GH1 | 95-39683.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/HXB17 | supernova_results/HXB17 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-01 | 2020-01-26 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39683.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1693885 |
| mean_dna_per_gem | 614351.2333 |
| bc_on_whitelist | 0.9155434389 |
| bc_mean_qscore | 36.41781376 |
| n50_linked_reads_per_molecule | 24 |
| corrected_loaded_mass_ng | 1.445184714 |
| snps_phased | 0.9008653093 |
| genes_phased_lt_100kb | 0.8738848337 |
| longest_phase_block | 2196026 |
| n50_phase_block | 124255 |
| molecule_length_mean | 32171.17946 |
| molecule_length_stddev | 52216.52566 |
| number_reads | 1334909172 |
| median_insert_size | 300 |
| mean_depth | 59.35075762 |
| zero_coverage | 0.02104943772 |
| mapped_reads | 0.9341463915 |
| pcr_duplication | 0.05727253944 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9506753922 |
| r1_q30_bases_fract | 0.9070660429 |
| r2_q20_bases_fract | 0.9345630845 |
| r2_q30_bases_fract | 0.8820009718 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9882145164 |
| bc_q30_bases_fract | 0.9659335784 |
| large_sv_calls | 2673 |
| short_deletion_calls | 34067 |
Deepvariant results
| index | 639 | 640 | 641 | 642 | 643 | 644 | 645 | 646 | 647 | 648 | 649 | 650 | 651 | 652 | 653 | 654 | 655 | 656 | 657 | 658 | 659 | 660 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.DV1 | 95-39683.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 | 35280 | 19224 | 23951 | 49048 | 32126 | 27417 | 39914 | 25310 | 36095 | 29755 | 85893 | 23769 | 90577 | 69403 | 75480 | 72884 | 39219 | 47010 | 61254 | 51803 | 43455 | 405 |
| Biallelic_Insertion | 34392 | 19299 | 21698 | 44677 | 30256 | 26197 | 35990 | 23829 | 32747 | 26196 | 79557 | 21666 | 84242 | 63549 | 68031 | 66147 | 37666 | 44468 | 55101 | 46898 | 42265 | 564 |
| Biallelic_SNP | 89474 | 29083 | 55779 | 206245 | 79451 | 52456 | 162782 | 36320 | 138378 | 110437 | 301767 | 62592 | 383039 | 277706 | 330252 | 277289 | 75697 | 176113 | 256031 | 216872 | 81319 | 2865 |
| Multiallelic_Complex | 972 | 420 | 497 | 968 | 692 | 618 | 803 | 537 | 768 | 718 | 2157 | 467 | 2052 | 1502 | 1598 | 1444 | 819 | 1296 | 1430 | 1179 | 740 | 13 |
| Multiallelic_Deletion | 1234 | 440 | 567 | 1917 | 763 | 501 | 1461 | 347 | 1400 | 1236 | 2992 | 654 | 2974 | 2691 | 3203 | 2562 | 777 | 1581 | 2892 | 2018 | 913 | 32 |
| Multiallelic_Insertion | 2469 | 793 | 1313 | 3512 | 1417 | 882 | 2771 | 804 | 2663 | 2362 | 5575 | 1367 | 5664 | 5192 | 5945 | 4977 | 1600 | 3127 | 5575 | 3920 | 1505 | 61 |
| Multiallelic_SNP | 47 | 34 | 51 | 82 | 58 | 83 | 123 | 63 | 69 | 153 | 292 | 29 | 270 | 168 | 119 | 126 | 97 | 195 | 133 | 176 | 70 | 2 |
| RefCall | 234736 | 159919 | 159587 | 253577 | 225633 | 229933 | 211138 | 197850 | 184934 | 185950 | 654368 | 135723 | 598999 | 398872 | 391048 | 384159 | 287534 | 341685 | 311281 | 297215 | 422192 | 28354 |
| Transition | 54483 | 14852 | 31754 | 119670 | 43910 | 26231 | 101710 | 17192 | 87971 | 69155 | 177198 | 37471 | 226751 | 171556 | 205424 | 168199 | 39083 | 103995 | 165613 | 134282 | 41199 | 1509 |
| Transversion | 34991 | 14231 | 24025 | 86575 | 35541 | 26225 | 61072 | 19128 | 50407 | 41282 | 124569 | 25121 | 156288 | 106150 | 124828 | 109090 | 36614 | 72118 | 90418 | 82590 | 40120 | 1356 |
Supernova results
| Analysis_ID | 95-39683.SN1 |
|---|---|
| assembly_size | 2479115258 |
| barcode_fraction | 1 |
| bases_per_read | 137.344 |
| bridge_1_50 | 42.251 |
| bridge_50 | 0.069 |
| bridge_model_badness_of_fit | 1.07368 |
| checksum | -9.87694e+17 |
| contig_N50 | 33850 |
| dinucleotide_percent | 1.40148 |
| dup_perc | 16.2885 |
| edge_N50 | 7649 |
| effective_coverage | 45.4552 |
| est_genome_size | 3140000000 |
| gc_percent | 42.2213 |
| hetdist | 34070 |
| high_AT_index | 0.0724177 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 25291.8 |
| m10 | 3.06738 |
| median_ins_sz | 318 |
| nreads | 1334909172 |
| p10 | 50.0588 |
| phase_block_N50 | 108864 |
| placed_perc | 57.2263 |
| proper_pairs_perc | 92.3861 |
| q30_r2_perc | 88.2001 |
| raw_coverage | 63.1957 |
| read_rate_DF_1_threaded | 34.3748 |
| read_rate_IO_10_threaded | 2719.65 |
| read_rate_IO_1_threaded | 2429.67 |
| repfrac | 10.4008 |
| rpb_N50 | 1010 |
| scaffold_N50 | 4062673 |
| scaffolds_10kb_plus | 7959 |
| scaffolds_1kb_plus | 42548 |
| unbar_perc | 8.44566 |
| valid_bc_perc | 91.5543 |