Detailed view of 95-39681
Strain
| ID | 58 |
|---|---|
| Name | HXB13 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB13_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0526 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0526 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 30 |
| 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 | 95-39681 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 101 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39681.LR1 | 95-39681.SN1 | 95-39681.GH1 | 95-39681.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/HXB13 | supernova_results/HXB13 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-26 | 2020-01-30 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39681.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1624182 |
| mean_dna_per_gem | 497019.8233 |
| bc_on_whitelist | 0.9219453599 |
| bc_mean_qscore | 36.43989109 |
| n50_linked_reads_per_molecule | 24 |
| corrected_loaded_mass_ng | 1.169177194 |
| snps_phased | 0.8968715729 |
| genes_phased_lt_100kb | 0.8188649397 |
| longest_phase_block | 1374648 |
| n50_phase_block | 75076 |
| molecule_length_mean | 29408.64359 |
| molecule_length_stddev | 57040.37618 |
| number_reads | 1435937618 |
| median_insert_size | 288 |
| mean_depth | 63.08767686 |
| zero_coverage | 0.02056581856 |
| mapped_reads | 0.9299621859 |
| pcr_duplication | 0.06606987743 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9473235082 |
| r1_q30_bases_fract | 0.9027323895 |
| r2_q20_bases_fract | 0.9304153117 |
| r2_q30_bases_fract | 0.8769587115 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9887322481 |
| bc_q30_bases_fract | 0.9671941415 |
| large_sv_calls | 3522 |
| short_deletion_calls | 31858 |
Deepvariant results
| index | 595 | 596 | 597 | 598 | 599 | 600 | 601 | 602 | 603 | 604 | 605 | 606 | 607 | 608 | 609 | 610 | 611 | 612 | 613 | 614 | 615 | 616 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.DV1 | 95-39681.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 | 32137 | 29546 | 24589 | 48767 | 27839 | 46020 | 35462 | 30359 | 30621 | 22650 | 71292 | 19051 | 109586 | 55834 | 77479 | 50619 | 57038 | 62816 | 61991 | 51383 | 48237 | 433 |
| Biallelic_Insertion | 31805 | 28286 | 22389 | 44659 | 27398 | 42320 | 32369 | 27799 | 28117 | 20869 | 68498 | 17807 | 100464 | 52539 | 69954 | 47877 | 52943 | 57493 | 55807 | 46606 | 47158 | 584 |
| Biallelic_SNP | 67383 | 117450 | 56603 | 205316 | 51283 | 213872 | 129161 | 71696 | 94343 | 64330 | 201667 | 27954 | 523789 | 182693 | 347799 | 101424 | 235199 | 303429 | 267530 | 213729 | 113468 | 2862 |
| Multiallelic_Complex | 859 | 660 | 560 | 974 | 618 | 1059 | 760 | 644 | 669 | 519 | 1833 | 392 | 2507 | 1345 | 1765 | 1047 | 1218 | 1640 | 1521 | 1245 | 921 | 12 |
| Multiallelic_Deletion | 919 | 1044 | 665 | 1933 | 521 | 1729 | 1210 | 832 | 1094 | 521 | 1790 | 296 | 4578 | 1839 | 3540 | 1079 | 2194 | 2966 | 3122 | 2192 | 1357 | 36 |
| Multiallelic_Insertion | 2002 | 2034 | 1478 | 3621 | 1020 | 3117 | 2263 | 1634 | 2080 | 1160 | 3432 | 738 | 8509 | 3561 | 6482 | 2224 | 4006 | 5431 | 5755 | 4075 | 2296 | 60 |
| Multiallelic_SNP | 42 | 47 | 62 | 93 | 62 | 155 | 88 | 86 | 43 | 98 | 278 | 20 | 346 | 155 | 124 | 78 | 321 | 277 | 150 | 197 | 91 | 1 |
| RefCall | 227470 | 182971 | 160399 | 257215 | 221225 | 268295 | 200437 | 205585 | 172872 | 172321 | 631760 | 127367 | 638897 | 380127 | 394127 | 341025 | 386148 | 372477 | 311456 | 297632 | 459349 | 27861 |
| Transition | 39216 | 70786 | 32600 | 118997 | 25265 | 130250 | 79276 | 42359 | 58508 | 36111 | 107939 | 14600 | 321299 | 108727 | 217769 | 55678 | 139372 | 188234 | 172474 | 131934 | 59814 | 1511 |
| Transversion | 28167 | 46664 | 24003 | 86319 | 26018 | 83622 | 49885 | 29337 | 35835 | 28219 | 93728 | 13354 | 202490 | 73966 | 130030 | 45746 | 95827 | 115195 | 95056 | 81795 | 53654 | 1351 |
Supernova results
| Analysis_ID | 95-39681.SN1 |
|---|---|
| assembly_size | 2462540520 |
| barcode_fraction | 1 |
| bases_per_read | 137.198 |
| bridge_1_50 | 302.861 |
| bridge_50 | 0.012 |
| bridge_model_badness_of_fit | 1.12936 |
| checksum | -2.17209e+18 |
| contig_N50 | 32757 |
| dinucleotide_percent | 1.41576 |
| dup_perc | 17.8517 |
| edge_N50 | 6926 |
| effective_coverage | 46.5536 |
| est_genome_size | 3220000000 |
| gc_percent | 42.1559 |
| hetdist | 22133 |
| high_AT_index | 0.0717753 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 17157.2 |
| m10 | 3.07766 |
| median_ins_sz | 310 |
| nreads | 1435937618 |
| p10 | 17.4412 |
| phase_block_N50 | 34034 |
| placed_perc | 56.1186 |
| proper_pairs_perc | 92.0616 |
| q30_r2_perc | 87.6959 |
| raw_coverage | 66.2149 |
| read_rate_DF_1_threaded | 34.2366 |
| read_rate_IO_10_threaded | 3093.2 |
| read_rate_IO_1_threaded | 3837.17 |
| repfrac | 11.2474 |
| rpb_N50 | 1064 |
| scaffold_N50 | 985068 |
| scaffolds_10kb_plus | 10021 |
| scaffolds_1kb_plus | 44662 |
| unbar_perc | 7.80546 |
| valid_bc_perc | 92.1945 |