Detailed view of 95-39675
Strain
| ID | 62 |
|---|---|
| Name | HXB2 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB2_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0520 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0520 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 28.4 |
| 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 | 95-39675 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 104 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39675.LR1 | 95-39675.SN1 | 95-39675.GH1 | 95-39675.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/HXB2 | supernova_results/HXB2 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-12 | 2020-01-30 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39675.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1506812 |
| mean_dna_per_gem | 871405.1988 |
| bc_on_whitelist | 0.9245957709 |
| bc_mean_qscore | 36.41180985 |
| n50_linked_reads_per_molecule | 26 |
| corrected_loaded_mass_ng | 2.049872133 |
| snps_phased | 0.8883309733 |
| genes_phased_lt_100kb | 0.9157699443 |
| longest_phase_block | 2721342 |
| n50_phase_block | 272419 |
| molecule_length_mean | 42043.59158 |
| molecule_length_stddev | 59050.56159 |
| number_reads | 1484848228 |
| median_insert_size | 307 |
| mean_depth | 67.73260296 |
| zero_coverage | 0.0206368654 |
| mapped_reads | 0.9490713323 |
| pcr_duplication | 0.06392721515 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9575462397 |
| r1_q30_bases_fract | 0.9162168 |
| r2_q20_bases_fract | 0.9461449567 |
| r2_q30_bases_fract | 0.8972194415 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9881903146 |
| bc_q30_bases_fract | 0.9654142424 |
| large_sv_calls | 2401 |
| short_deletion_calls | 38111 |
Deepvariant results
| index | 881 | 882 | 883 | 884 | 885 | 886 | 887 | 888 | 889 | 890 | 891 | 892 | 893 | 894 | 895 | 896 | 897 | 898 | 899 | 900 | 901 | 902 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.DV1 | 95-39675.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 | 37565 | 28113 | 32005 | 49428 | 43566 | 34921 | 37532 | 38744 | 22509 | 28909 | 114644 | 24078 | 69064 | 73256 | 64709 | 62012 | 49176 | 43548 | 50666 | 52478 | 56602 | 405 |
| Biallelic_Insertion | 35345 | 26295 | 27835 | 44555 | 39331 | 31980 | 33540 | 34503 | 21347 | 25226 | 102797 | 21327 | 64630 | 66232 | 58259 | 56159 | 44998 | 40455 | 45718 | 46769 | 51687 | 526 |
| Biallelic_SNP | 104181 | 99132 | 106593 | 205929 | 173483 | 115200 | 142441 | 134314 | 35772 | 107202 | 534484 | 72359 | 184423 | 307979 | 234425 | 184204 | 166164 | 144992 | 172523 | 218726 | 166701 | 2919 |
| Multiallelic_Complex | 882 | 547 | 706 | 967 | 929 | 752 | 735 | 801 | 420 | 700 | 2670 | 504 | 1510 | 1498 | 1383 | 1196 | 1073 | 1059 | 1115 | 1147 | 1002 | 16 |
| Multiallelic_Deletion | 1342 | 890 | 1330 | 1854 | 1348 | 844 | 1262 | 1244 | 433 | 1213 | 5085 | 630 | 1709 | 2900 | 2583 | 1852 | 1534 | 1376 | 2087 | 1976 | 2090 | 41 |
| Multiallelic_Insertion | 2745 | 1729 | 2483 | 3474 | 2583 | 1587 | 2348 | 2504 | 869 | 2140 | 9308 | 1196 | 3272 | 5537 | 4778 | 3507 | 2950 | 2710 | 3976 | 3845 | 3523 | 48 |
| Multiallelic_SNP | 69 | 49 | 70 | 92 | 109 | 99 | 104 | 119 | 27 | 192 | 455 | 103 | 187 | 185 | 96 | 84 | 289 | 150 | 120 | 192 | 112 | 2 |
| RefCall | 229243 | 163958 | 169015 | 232194 | 237333 | 229843 | 192390 | 213252 | 145215 | 175536 | 679982 | 146331 | 506555 | 385352 | 335956 | 333270 | 350579 | 311428 | 266833 | 280832 | 470615 | 28810 |
| Transition | 64255 | 59843 | 67782 | 119425 | 106631 | 64940 | 87577 | 84769 | 19217 | 66430 | 329301 | 43007 | 103825 | 190212 | 145489 | 108790 | 96075 | 85888 | 108859 | 135284 | 90421 | 1556 |
| Transversion | 39926 | 39289 | 38811 | 86504 | 66852 | 50260 | 54864 | 49545 | 16555 | 40772 | 205183 | 29352 | 80598 | 117767 | 88936 | 75414 | 70089 | 59104 | 63664 | 83442 | 76280 | 1363 |
Supernova results
| Analysis_ID | 95-39675.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 |