Detailed view of 4512-JFI-0581
Strain
| ID | 11 |
|---|---|
| Name | FHH/EurMcwi |
| Type | Inbred |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | FHH/EurMcwi_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | None |
| Euthanasia_date | None |
| Source | Geurts |
| Note | None |
Tissue
| ID | 4512-JFI-0577 |
|---|---|
| Type | spleen |
| Transfer_History | Geurts to Chen |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0577 |
|---|---|
| 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-0581 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 74 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 4512-JFI-0581.LR1 | 4512-JFI-0581.SN1 | 4512-JFI-0581.DV1 |
|---|---|---|---|
| Software_name | LongRanger | Supernova | DeepVariant |
| Software_version | 2.2.2 | 2.1.3 | 0.9.0-gpu |
| Results_dir | longranger_results/0581_fhh | supernova_results/fhh_denovo_multi | /data/10_TB/deepvar |
| Analysis_date | 2019-04-02 | 2019-04-26 | 2019-12-04 |
| Note | combined analysis of 4512-JFI-0581 and 4512-JFI-0582 |
LongRanger results
| Analysis_ID | 4512-JFI-0581.LR1 |
|---|---|
| instrument_ids | E00332 |
| gems_detected | 1676155 |
| mean_dna_per_gem | 601504.2872 |
| bc_on_whitelist | 0.9248393305 |
| bc_mean_qscore | 38.1065217 |
| n50_linked_reads_per_molecule | 6 |
| corrected_loaded_mass_ng | 1.414963874 |
| snps_phased | 0.8780370205 |
| genes_phased_lt_100kb | 0.5956808638 |
| longest_phase_block | 383089 |
| n50_phase_block | 25357 |
| molecule_length_mean | 15897.96963 |
| molecule_length_stddev | 45969.59835 |
| number_reads | 813670506 |
| median_insert_size | 271 |
| mean_depth | 36.21217131 |
| zero_coverage | 0.02441035231 |
| mapped_reads | 0.9460076607 |
| pcr_duplication | 0.04066877759 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9434754676 |
| r1_q30_bases_fract | 0.8848712744 |
| r2_q20_bases_fract | 0.8823811054 |
| r2_q30_bases_fract | 0.7895214626 |
| si_q20_bases_fract | 0.9608293658 |
| si_q30_bases_fract | 0.9299658491 |
| bc_q20_bases_fract | 0.9902218482 |
| bc_q30_bases_fract | 0.9711692307 |
| large_sv_calls | 1961 |
| short_deletion_calls | 27357 |
Deepvariant results
| index | 265 | 266 | 267 | 268 | 269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.DV1 | 4512-JFI-0581.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 | 49337 | 31577 | 33337 | 49271 | 50980 | 40807 | 37807 | 44112 | 36598 | 31287 | 112728 | 30888 | 118954 | 76527 | 74017 | 84438 | 61588 | 63013 | 53037 | 52675 | 52709 | 452 |
| Biallelic_Insertion | 50427 | 32353 | 31274 | 48110 | 49163 | 40865 | 36466 | 41749 | 35850 | 29713 | 110167 | 29617 | 114171 | 75003 | 72039 | 81284 | 61019 | 61738 | 53508 | 51217 | 52281 | 623 |
| Biallelic_SNP | 176323 | 124838 | 125130 | 196556 | 237894 | 162589 | 146075 | 181005 | 145213 | 122262 | 521471 | 129162 | 629785 | 328053 | 330797 | 372502 | 247444 | 289904 | 201448 | 225718 | 139345 | 2784 |
| Multiallelic_Complex | 1650 | 809 | 932 | 1270 | 1376 | 1113 | 959 | 1194 | 933 | 960 | 3255 | 777 | 3189 | 2052 | 1913 | 2121 | 1589 | 1803 | 1480 | 1517 | 919 | 18 |
| Multiallelic_Deletion | 3435 | 1523 | 1791 | 2569 | 2700 | 1793 | 1682 | 2520 | 1968 | 1711 | 6455 | 1464 | 6589 | 4489 | 4129 | 4785 | 3235 | 3761 | 3049 | 2868 | 1749 | 32 |
| Multiallelic_Insertion | 5629 | 2666 | 3111 | 4275 | 4565 | 2961 | 2895 | 4126 | 3259 | 2918 | 10743 | 2450 | 11331 | 7716 | 6884 | 8074 | 5550 | 6543 | 5171 | 4721 | 2667 | 66 |
| Multiallelic_SNP | 106 | 54 | 143 | 91 | 173 | 150 | 89 | 132 | 52 | 219 | 504 | 127 | 496 | 248 | 198 | 183 | 206 | 203 | 133 | 183 | 113 | 5 |
| RefCall | 369327 | 253089 | 226757 | 339171 | 362035 | 329400 | 271764 | 315896 | 256711 | 242471 | 933594 | 213348 | 895134 | 567997 | 545904 | 567301 | 461560 | 480812 | 397692 | 391139 | 475436 | 28136 |
| Transition | 114177 | 77515 | 79485 | 119462 | 147458 | 96819 | 89575 | 116256 | 92041 | 76753 | 321808 | 81469 | 383352 | 206094 | 204617 | 233270 | 151270 | 182832 | 128751 | 140562 | 76275 | 1476 |
| Transversion | 62146 | 47323 | 45645 | 77094 | 90436 | 65770 | 56500 | 64749 | 53172 | 45509 | 199663 | 47693 | 246433 | 121959 | 126180 | 139232 | 96174 | 107072 | 72697 | 85156 | 63070 | 1308 |
Supernova results
| Analysis_ID | 4512-JFI-0581.SN1 |
|---|---|
| assembly_size | 2410523052 |
| barcode_fraction | 1 |
| bases_per_read | 139.5 |
| bridge_1_50 | 254.313 |
| bridge_50 | 0.004 |
| bridge_model_badness_of_fit | 1.0591 |
| checksum | 6.78604635042457e+18 |
| contig_N50 | 32208 |
| dinucleotide_percent | 1.82553 |
| dup_perc | 14.4144 |
| edge_N50 | 7935 |
| effective_coverage | 41.0917 |
| est_genome_size | 3260000000 |
| gc_percent | 42.0004 |
| hetdist | 28395 |
| high_AT_index | 0.0740349 |
| likely_sequencers | HiSeq X |
| lw_mean_mol_len | 15844.4 |
| m10 | 2.95545 |
| median_ins_sz | 289 |
| nreads | 1200041596 |
| p10 | 17.6176 |
| phase_block_N50 | 27624 |
| placed_perc | 61.7185 |
| proper_pairs_perc | 87.855 |
| q30_r2_perc | 78.7337 |
| raw_coverage | 55.6616 |
| read_rate_DF_1_threaded | 37.713 |
| read_rate_IO_10_threaded | 3112.11 |
| read_rate_IO_1_threaded | 3782.92 |
| repfrac | 11.0596 |
| rpb_N50 | 440 |
| scaffold_N50 | 952568 |
| scaffolds_10kb_plus | 9428 |
| scaffolds_1kb_plus | 37650 |
| unbar_perc | 7.75831 |
| valid_bc_perc | 92.2417 |