Detailed view of 95-39691

Strain

ID 69
Name HXB27
Type RI
Living False
Source
Note

Animal

Animal_name HXB27_Rat1
Sex M
Age adult
Generation
Euthanasia_date 2018-08-01
Source Pravenec
Note

Tissue

ID 4512-JFI-0536
Type spleen
Transfer_History Pravenec to Chen to HudsonAlpha
Note None

Sequencing

DNA_source 4512-JFI-0536
Platform 10X Chromium
DNA_extraction_method HMW
DNA_concentration 37.4
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 95-39691
Raw_data_format fastq.gz
Raw_data_file_size_GB 35
Raw_data_available_from Chen
Note None

Analysis

Analysis_ID 95-39691.LR1 95-39691.SN1 95-39691.GH1 95-39691.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/HXB27 supernova_results/HXB27 grocsvs_HXB /data/10_TB/deepvar
Analysis_date 2019-10-06 2020-01-22 2020-03-02 2019-12-04
Note combined analysis of BN samples and HXB

LongRanger results

Analysis_ID 95-39691.LR1
instrument_ids A00735
gems_detected 1815712
mean_dna_per_gem 585841.2128
bc_on_whitelist 0.90816507
bc_mean_qscore 36.41103486
n50_linked_reads_per_molecule 6
corrected_loaded_mass_ng 1.378118444
snps_phased 0.8648657753
genes_phased_lt_100kb 0.7105203363
longest_phase_block 784392
n50_phase_block 68636
molecule_length_mean 23772.65072
molecule_length_stddev 36257.96529
number_reads 493960000
median_insert_size 320
mean_depth 21.71887193
zero_coverage 0.02475056489
mapped_reads 0.9275177828
pcr_duplication 0.02724942756
on_target_bases
r1_q20_bases_fract 0.9457377276
r1_q30_bases_fract 0.8998085587
r2_q20_bases_fract 0.9264294472
r2_q30_bases_fract 0.8706050061
si_q20_bases_fract NaN
si_q30_bases_fract NaN
bc_q20_bases_fract 0.9881428542
bc_q30_bases_fract 0.9653620556
large_sv_calls 1867
short_deletion_calls 24942

Deepvariant results

index 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858
Analysis_ID 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.DV1 95-39691.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 45739 18883 23126 30143 30454 38324 28102 38198 36246 25240 66865 25634 61085 45115 65900 55415 53675 43258 33327 42599 44508 409
Biallelic_Insertion 46069 21101 22384 31190 31563 38177 27985 36228 35148 24208 70895 24902 65409 47954 64527 55299 53508 44688 35506 41851 39784 465
Biallelic_SNP 144089 22210 50580 34969 61880 138929 61911 125199 136921 78015 147330 80071 113900 84754 242250 112431 190869 146750 49222 131999 131488 2544
Multiallelic_Complex 996 397 461 533 643 743 544 759 711 515 1599 457 1286 928 1247 1045 1066 1095 721 908 470 6
Multiallelic_Deletion 2132 232 388 404 461 954 503 1122 1305 644 1125 613 877 624 2389 1418 1571 1039 534 1195 667 18
Multiallelic_Insertion 3544 362 806 672 838 1664 934 2071 2158 1151 2037 1169 1532 1124 3797 2204 2731 1873 974 2144 1081 31
Multiallelic_SNP 78 26 40 23 47 78 49 90 49 129 150 27 159 79 82 67 269 183 43 112 67 20456
RefCall 334938 183927 174906 243715 248424 279197 213235 267575 229806 192847 671358 166888 577307 401728 448969 409829 424336 377871 297874 317475 256054 1338
Transition 92822 10260 28687 16580 33874 80841 35430 79299 87207 46706 78104 49152 57790 43447 149383 66820 112322 83815 25155 79970 70771 1206
Transversion 51267 11950 21893 18389 28006 58088 26481 45900 49714 31309 69226 30919 56110 41307 92867 45611 78547 62935 24067 52029 60717

Supernova results

Analysis_ID 95-39691.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