Detailed view of 4512-JFI-0579
Strain
| ID | 31 |
|---|---|
| Name | SS/JrHsdMcwi |
| Type | Inbred |
| Living | False |
| Source | MCW |
| Note |
Animal
| Animal_name | SS/JrHsdMcwi_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | |
| Source | Geurts |
| Note |
Tissue
| ID | 4512-JFI-0575 |
|---|---|
| Type | spleen |
| Transfer_History | Geurts to Chen |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0575 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | |
| DNA_target_length | |
| DNA_extraction_facility | HudsonAlpha |
| Library_kit | 150bp_PE |
| Library_facility | HudsonAlpha |
| Sequencing_instrument | NovaSeq |
| Sequencing_date | 2018-10-12 |
| Sequencing_facility | HudsonAlpha |
| Sequencing_notes | S4 |
| Raw_data_dir_name | 4512-JFI-0579 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 77 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0579.LR1 | 4512-JFI-0579.SN1 | 4512-JFI-0579.DV1 |
|---|---|---|---|
| Software_name | LongRanger | Supernova | DeepVariant |
| Software_version | 2.2.2 | 2.1.1 | 0.9.0-gpu |
| Results_dir | longranger_results/0579_dss | supernova_results/dss_denovo_multi | /data/10_TB/deepvar |
| Analysis_date | 2019-03-29 | 2019-04-24 | 2019-12-04 |
| Note | combined analysis of 4512-JFI-0579 and 4512-JFI-0580 |
LongRanger results
| Analysis_ID | 4512-JFI-0579.LR1 |
|---|---|
| instrument_ids | E00364 |
| gems_detected | 1614707 |
| mean_dna_per_gem | 501108.8997 |
| bc_on_whitelist | 0.9240389403 |
| bc_mean_qscore | 38.02369398 |
| n50_linked_reads_per_molecule | 5 |
| corrected_loaded_mass_ng | 1.178796236 |
| snps_phased | 0.8690549569 |
| genes_phased_lt_100kb | 0.568288519 |
| longest_phase_block | 371255 |
| n50_phase_block | 22028 |
| molecule_length_mean | 13310.15126 |
| molecule_length_stddev | 48156.54593 |
| number_reads | 790802712 |
| median_insert_size | 265 |
| mean_depth | 33.68942901 |
| zero_coverage | 0.02429804402 |
| mapped_reads | 0.927868042 |
| pcr_duplication | 0.04573654649 |
| on_target_bases | |
| r1_q20_bases_fract | 0.8709591578 |
| r1_q30_bases_fract | 0.7595539468 |
| r2_q20_bases_fract | 0.8534921844 |
| r2_q30_bases_fract | 0.7416727298 |
| si_q20_bases_fract | 0.9541505265 |
| si_q30_bases_fract | 0.9204502431 |
| bc_q20_bases_fract | 0.9892417478 |
| bc_q30_bases_fract | 0.9659714816 |
| large_sv_calls | 2125 |
| short_deletion_calls | 26436 |
Deepvariant results
| index | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.DV1 | 4512-JFI-0579.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 | 49136 | 33921 | 33353 | 46634 | 51196 | 43919 | 36675 | 44746 | 36521 | 27271 | 107306 | 30972 | 117134 | 72728 | 73800 | 81798 | 64679 | 62595 | 53441 | 48153 | 51242 | 476 |
| Biallelic_Insertion | 50741 | 34589 | 31206 | 46631 | 50373 | 44395 | 36665 | 43031 | 36414 | 27151 | 108557 | 29733 | 115048 | 73633 | 73958 | 80392 | 64671 | 62377 | 54182 | 48575 | 50580 | 605 |
| Biallelic_SNP | 175876 | 143757 | 125834 | 172030 | 238904 | 183498 | 134534 | 187252 | 140765 | 94582 | 490156 | 128657 | 598206 | 294218 | 315875 | 349424 | 270043 | 288221 | 197277 | 187674 | 136264 | 2788 |
| Multiallelic_Complex | 1457 | 846 | 886 | 1142 | 1233 | 1133 | 884 | 1150 | 871 | 738 | 2903 | 755 | 2854 | 1843 | 1778 | 1897 | 1571 | 1643 | 1382 | 1281 | 768 | 19 |
| Multiallelic_Deletion | 2907 | 1624 | 1738 | 2092 | 2312 | 1802 | 1447 | 2259 | 1818 | 1231 | 5356 | 1314 | 5789 | 3590 | 3822 | 4027 | 3129 | 3394 | 2929 | 2167 | 1231 | 22 |
| Multiallelic_Insertion | 4726 | 2719 | 2905 | 3427 | 3934 | 3103 | 2422 | 3670 | 2999 | 2005 | 8729 | 2322 | 9656 | 6158 | 6153 | 6889 | 5254 | 5658 | 4680 | 3508 | 1993 | 48 |
| Multiallelic_SNP | 80 | 63 | 126 | 78 | 164 | 135 | 90 | 158 | 63 | 161 | 446 | 136 | 427 | 186 | 132 | 143 | 208 | 204 | 113 | 188 | 90 | 30480 |
| RefCall | 428161 | 314965 | 257225 | 392351 | 430905 | 394342 | 308739 | 366835 | 308304 | 257227 | 1053922 | 242641 | 1038502 | 657926 | 641385 | 657630 | 560044 | 562606 | 473599 | 436482 | 564133 | 1477 |
| Transition | 114293 | 90798 | 80780 | 103260 | 149187 | 111713 | 83199 | 120167 | 89724 | 58390 | 301857 | 82125 | 366634 | 184273 | 196899 | 217849 | 166381 | 182376 | 127511 | 115053 | 73658 | 1311 |
| Transversion | 61583 | 52959 | 45054 | 68770 | 89717 | 71785 | 51335 | 67085 | 51041 | 36192 | 188299 | 46532 | 231572 | 109945 | 118976 | 131575 | 103662 | 105845 | 69766 | 72621 | 62606 |
Supernova results
| Analysis_ID | 4512-JFI-0579.SN1 |
|---|---|
| assembly_size | 2347096245 |
| barcode_fraction | 1 |
| bases_per_read | 139.5 |
| bridge_1_50 | 613.001 |
| bridge_50 | 0.001 |
| bridge_model_badness_of_fit | 1.15491 |
| checksum | -3.36528e+18 |
| contig_N50 | 29104 |
| dinucleotide_percent | 1.88374 |
| dup_perc | 16.1967 |
| edge_N50 | 8419 |
| effective_coverage | 37.8188 |
| est_genome_size | 3390000000 |
| gc_percent | 42.0033 |
| hetdist | 26705 |
| high_AT_index | 0.0728453 |
| likely_sequencers | HiSeq X |
| lw_mean_mol_len | 11755.3 |
| m10 | 4.78435 |
| median_ins_sz | 287 |
| nreads | 1200041504 |
| p10 | 10.2353 |
| phase_block_N50 | 19077 |
| placed_perc | 56.8112 |
| proper_pairs_perc | 86.9512 |
| q30_r2_perc | 75.6337 |
| raw_coverage | 53.5313 |
| read_rate_DF_1_threaded | 31.1879 |
| read_rate_IO_10_threaded | 2820.86 |
| read_rate_IO_1_threaded | 3216.68 |
| repfrac | 11.4985 |
| rpb_N50 | 460 |
| scaffold_N50 | 105985 |
| scaffolds_10kb_plus | 33638 |
| scaffolds_1kb_plus | 69589 |
| unbar_perc | 7.798 |
| valid_bc_perc | 92.202 |