Detailed view of 95-39678
Strain
| ID | 74 |
|---|---|
| Name | HXB5 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB5_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0523 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0523 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 31.2 |
| 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 | 95-39678 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 103 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39678.LR1 | 95-39678.SN1 | 95-39678.GH1 | 95-39678.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/HXB5 | supernova_results/HXB5 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-20 | 2020-01-30 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39678.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1569053 |
| mean_dna_per_gem | 651553.5653 |
| bc_on_whitelist | 0.9301362852 |
| bc_mean_qscore | 36.29474386 |
| n50_linked_reads_per_molecule | 15 |
| corrected_loaded_mass_ng | 1.532698563 |
| snps_phased | 0.8929116769 |
| genes_phased_lt_100kb | 0.8323688272 |
| longest_phase_block | 1497862 |
| n50_phase_block | 91811 |
| molecule_length_mean | 26504.75126 |
| molecule_length_stddev | 66028.70298 |
| number_reads | 1432147664 |
| median_insert_size | 329 |
| mean_depth | 64.82334092 |
| zero_coverage | 0.02236424212 |
| mapped_reads | 0.9445279604 |
| pcr_duplication | 0.08198435719 |
| on_target_bases | |
| r1_q20_bases_fract | 0.951645846 |
| r1_q30_bases_fract | 0.9058108851 |
| r2_q20_bases_fract | 0.9402677686 |
| r2_q30_bases_fract | 0.886397728 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.985556639 |
| bc_q30_bases_fract | 0.9588639569 |
| large_sv_calls | 2460 |
| short_deletion_calls | 34314 |
Deepvariant results
| index | 969 | 970 | 971 | 972 | 973 | 974 | 975 | 976 | 977 | 978 | 979 | 980 | 981 | 982 | 983 | 984 | 985 | 986 | 987 | 988 | 989 | 990 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.DV1 | 95-39678.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 | 54079 | 19477 | 34051 | 29857 | 50972 | 46121 | 28158 | 24996 | 37823 | 21673 | 109657 | 21578 | 91494 | 73239 | 75693 | 52111 | 46615 | 40428 | 42395 | 40220 | 56438 | 372 |
| Biallelic_Insertion | 49321 | 19510 | 29434 | 27757 | 45938 | 41985 | 25819 | 23349 | 33893 | 19844 | 99229 | 19545 | 84039 | 66851 | 68190 | 47768 | 43715 | 38718 | 39773 | 36909 | 52875 | 586 |
| Biallelic_SNP | 210520 | 33500 | 127047 | 34098 | 229082 | 212075 | 65364 | 33898 | 151264 | 51793 | 499150 | 51661 | 374038 | 319015 | 325636 | 92041 | 156845 | 131320 | 124949 | 126458 | 166497 | 2806 |
| Multiallelic_Complex | 1348 | 394 | 737 | 535 | 973 | 954 | 507 | 496 | 748 | 453 | 2542 | 420 | 1943 | 1433 | 1543 | 981 | 954 | 1069 | 871 | 902 | 986 | 17 |
| Multiallelic_Deletion | 3028 | 371 | 1437 | 536 | 2008 | 1648 | 604 | 333 | 1538 | 496 | 4552 | 468 | 2926 | 2804 | 3196 | 1307 | 1260 | 1105 | 1384 | 1228 | 2076 | 40 |
| Multiallelic_Insertion | 5571 | 753 | 2775 | 997 | 3646 | 2888 | 1227 | 712 | 2805 | 1021 | 8281 | 956 | 5733 | 5344 | 5772 | 2413 | 2329 | 2142 | 2696 | 2285 | 3483 | 50 |
| Multiallelic_SNP | 108 | 30 | 148 | 30 | 128 | 141 | 65 | 69 | 61 | 83 | 396 | 101 | 251 | 170 | 104 | 55 | 298 | 210 | 52 | 139 | 112 | 1 |
| RefCall | 275724 | 154558 | 182762 | 205122 | 258082 | 254344 | 180121 | 196067 | 183989 | 167577 | 696845 | 146635 | 562136 | 410610 | 378157 | 327660 | 362174 | 328327 | 271523 | 271917 | 477265 | 28625 |
| Transition | 137534 | 16948 | 81037 | 15807 | 142048 | 129576 | 37371 | 15604 | 96866 | 28904 | 305970 | 29416 | 225382 | 195754 | 203633 | 52400 | 88378 | 73352 | 76104 | 74389 | 90628 | 1496 |
| Transversion | 72986 | 16552 | 46010 | 18291 | 87034 | 82499 | 27993 | 18294 | 54398 | 22889 | 193180 | 22245 | 148656 | 123261 | 122003 | 39641 | 68467 | 57968 | 48845 | 52069 | 75869 | 1310 |
Supernova results
| Analysis_ID | 95-39678.SN1 |
|---|---|
| assembly_size | |
| barcode_fraction | |
| bases_per_read | |
| bridge_1_50 | |
| bridge_50 | |
| bridge_model_badness_of_fit | |
| checksum | |
| contig_N50 | |
| dinucleotide_percent | |
| dup_perc | |
| edge_N50 | |
| effective_coverage | |
| est_genome_size | |
| gc_percent | |
| hetdist | |
| high_AT_index | |
| likely_sequencers | |
| lw_mean_mol_len | |
| m10 | |
| median_ins_sz | |
| nreads | |
| p10 | |
| phase_block_N50 | |
| placed_perc | |
| proper_pairs_perc | |
| q30_r2_perc | |
| raw_coverage | |
| read_rate_DF_1_threaded | |
| read_rate_IO_10_threaded | |
| read_rate_IO_1_threaded | |
| repfrac | |
| rpb_N50 | |
| scaffold_N50 | |
| scaffolds_10kb_plus | |
| scaffolds_1kb_plus | |
| unbar_perc | |
| valid_bc_perc |