Detailed view of 95-39693
Strain
| ID | 72 |
|---|---|
| Name | HXB31 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB31_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0538 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0538 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 33.8 |
| 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 | 95-39693 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 79 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39693.LR1 | 95-39693.SN1 | 95-39693.GH1 | 95-39693.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/HXB31 | supernova_results/HXB31 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-10 | 2020-01-30 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39693.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1815085 |
| mean_dna_per_gem | 729054.7264 |
| bc_on_whitelist | 0.920280146 |
| bc_mean_qscore | 36.32934282 |
| n50_linked_reads_per_molecule | 13 |
| corrected_loaded_mass_ng | 1.715010386 |
| snps_phased | 0.8859751793 |
| genes_phased_lt_100kb | 0.8291529605 |
| longest_phase_block | 1243808 |
| n50_phase_block | 93394 |
| molecule_length_mean | 28333.04942 |
| molecule_length_stddev | 47763.95786 |
| number_reads | 1111841926 |
| median_insert_size | 306 |
| mean_depth | 50.19094664 |
| zero_coverage | 0.02076673979 |
| mapped_reads | 0.9429979348 |
| pcr_duplication | 0.04795891371 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9506984703 |
| r1_q30_bases_fract | 0.9048979445 |
| r2_q20_bases_fract | 0.9380824903 |
| r2_q30_bases_fract | 0.8852318015 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863187573 |
| bc_q30_bases_fract | 0.9606628349 |
| large_sv_calls | 1982 |
| short_deletion_calls | 32112 |
Deepvariant results
| index | 903 | 904 | 905 | 906 | 907 | 908 | 909 | 910 | 911 | 912 | 913 | 914 | 915 | 916 | 917 | 918 | 919 | 920 | 921 | 922 | 923 | 924 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.DV1 | 95-39693.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 | 33231 | 32388 | 22377 | 41484 | 43349 | 26753 | 29774 | 29659 | 30691 | 27256 | 85886 | 29741 | 95323 | 70944 | 59474 | 76473 | 59004 | 57384 | 57675 | 38628 | 50146 | 415 |
| Biallelic_Insertion | 33318 | 30457 | 20668 | 38520 | 40079 | 25789 | 27380 | 27851 | 28585 | 24377 | 81080 | 26870 | 89017 | 65265 | 55063 | 69014 | 54709 | 53329 | 52573 | 36325 | 47465 | 563 |
| Biallelic_SNP | 74243 | 134794 | 41989 | 134677 | 166198 | 48265 | 79685 | 69076 | 100523 | 95829 | 311322 | 117370 | 421818 | 272589 | 194181 | 285661 | 221290 | 257754 | 221580 | 107424 | 123674 | 2830 |
| Multiallelic_Complex | 892 | 679 | 493 | 856 | 856 | 627 | 571 | 618 | 572 | 641 | 2197 | 605 | 2100 | 1519 | 1303 | 1593 | 1168 | 1494 | 1350 | 853 | 826 | 10 |
| Multiallelic_Deletion | 982 | 1163 | 398 | 1306 | 1474 | 428 | 810 | 601 | 927 | 963 | 2747 | 982 | 3231 | 2817 | 2061 | 2951 | 2094 | 2340 | 2666 | 1106 | 1300 | 36 |
| Multiallelic_Insertion | 2088 | 2173 | 964 | 2355 | 2799 | 803 | 1416 | 1274 | 1778 | 1828 | 5244 | 1944 | 6101 | 5252 | 3819 | 5464 | 4190 | 4421 | 4845 | 2043 | 2060 | 54 |
| Multiallelic_SNP | 43 | 59 | 50 | 71 | 100 | 86 | 57 | 71 | 52 | 190 | 341 | 113 | 298 | 123 | 65 | 123 | 162 | 244 | 109 | 120 | 70 | 1 |
| RefCall | 259977 | 207645 | 165582 | 261287 | 270147 | 248399 | 202794 | 216996 | 193353 | 196616 | 710429 | 181270 | 659679 | 437209 | 387214 | 431557 | 357115 | 395123 | 338149 | 284411 | 444935 | 28593 |
| Transition | 43925 | 82800 | 22505 | 76918 | 100056 | 23200 | 46751 | 39539 | 62021 | 59334 | 180987 | 73615 | 250903 | 170623 | 118749 | 177935 | 134468 | 159110 | 143671 | 62763 | 65137 | 1496 |
| Transversion | 30318 | 51994 | 19484 | 57759 | 66142 | 25065 | 32934 | 29537 | 38502 | 36495 | 130335 | 43755 | 170915 | 101966 | 75432 | 107726 | 86822 | 98644 | 77909 | 44661 | 58537 | 1334 |
Supernova results
| Analysis_ID | 95-39693.SN1 |
|---|---|
| assembly_size | 2447789287 |
| barcode_fraction | 1 |
| bases_per_read | 137.649 |
| bridge_1_50 | 47.171 |
| bridge_50 | 0.034 |
| bridge_model_badness_of_fit | 1.02403 |
| checksum | 5.416438013436275e+18 |
| contig_N50 | 36394 |
| dinucleotide_percent | 1.19922 |
| dup_perc | 15.6395 |
| edge_N50 | 8756 |
| effective_coverage | 39.1508 |
| est_genome_size | 3080000000 |
| gc_percent | 41.9914 |
| hetdist | 51699 |
| high_AT_index | 0.0757786 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 25544.8 |
| m10 | 2.63588 |
| median_ins_sz | 321 |
| nreads | 1111841926 |
| p10 | 47.4412 |
| phase_block_N50 | 28619 |
| placed_perc | 63.2312 |
| proper_pairs_perc | 92.578 |
| q30_r2_perc | 88.5232 |
| raw_coverage | 53.764 |
| read_rate_DF_1_threaded | 6.88363 |
| read_rate_IO_10_threaded | 2208.23 |
| read_rate_IO_1_threaded | 2158.54 |
| repfrac | 10.1466 |
| rpb_N50 | 758 |
| scaffold_N50 | 4759820 |
| scaffolds_10kb_plus | 4937 |
| scaffolds_1kb_plus | 33551 |
| unbar_perc | 7.97199 |
| valid_bc_perc | 92.028 |