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Short_reads_raw_and_trimmedData
Long_reads_PacBio_Iso-Seq
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| # Illumina and Solid raw reads pre-processing | |||||||||||||||||
| # CLC Genomics Workbench 6-10 | |||||||||||||||||
| # parameters used for trimming # Removal of low quality sequences (limit = 0.05). # Removal of ambiguous nucleotides: No ambiguous nucleotides allowed. # Removal of adapter sequences and polyA. # Removal of sequences on length: minimum length 16 nucleotides and maximum length 1,000 nucleotides. | |||||||||||||||||
| Cultivar | SampleID | Number of reads | Avg.length | Number of reads after trim | Percentage trimmed | Avg.length after trim | Sequencing technology | Library type | SRA ID | Tissue | Inoculation/infestation/treatment | Days post inoculation/infestation/treatment | Plants growth conditions | Vectors or transgenic elements present | Orientation of reads in pair | Read strandness | Data Source |
| Desiree | Desiree_PVY_l1_1 | 53899470 | 90 | 53899470 | 1 | 89.9 | Illumina | DSN PE90 unstranded | SRR10070125 | leaf | PVY | na | growth chamber | na | fr | both | NIB |
| Desiree | CONT_coi1 | 49158746 | 90 | 49158746 | 1 | 90 | Illumina | PE90 unstranded | SRR1207288 | leaf | control | 1 | growth chamber | coi1-RNAi element | fr | both | NIB |
| Desiree | CONT_NT | 48679626 | 90 | 48679626 | 1 | 90 | Illumina | PE90 unstranded | SRR1207290 | leaf | control | 1 | growth chamber | na | fr | both | NIB |
| Desiree | CPB_coi1 | 47988790 | 90 | 47988790 | 1 | 90 | Illumina | PE90 unstranded | SRR1207287 | leaf | CPB | 1 | growth chamber | coi1-RNAi element | fr | both | NIB |
| Desiree | CPB_NT | 49224502 | 90 | 49224502 | 1 | 90 | Illumina | PE90 unstranded | SRR1207289 | leaf | CPB | 1 | growth chamber | na | fr | both | NIB |
| Desiree | SRR3161991 | 11642703 | 49 | 11596396 | 0.9960226589993749 | 47.3 | Illumina | SE50 unstranded | SRR3161991 | leaf | control | na | field | na | na | both | ENA |
| Desiree | SRR3161995 | 11742842 | 49 | 11713708 | 0.997518999233746 | 48 | Illumina | SE50 unstranded | SRR3161995 | leaf | drought | na | field | na | na | both | ENA |
| Desiree | SRR3161999 | 11835090 | 49 | 11787063 | 0.9959419826972165 | 47.2 | Illumina | SE50 unstranded | SRR3161999 | leaf | control | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162003 | 12066501 | 49 | 12023318 | 0.9964212492088634 | 47.5 | Illumina | SE50 unstranded | SRR3162003 | leaf | drought | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162007 | 12412385 | 49 | 12368684 | 0.9964792423051654 | 47.5 | Illumina | SE50 unstranded | SRR3162007 | leaf | control | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162011 | 11869495 | 49 | 11840459 | 0.9975537291182144 | 48 | Illumina | SE50 unstranded | SRR3162011 | leaf | drought | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162015 | 12319733 | 49 | 12286870 | 0.9973324908908334 | 47.9 | Illumina | SE50 unstranded | SRR3162015 | leaf | control | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162019 | 11823475 | 49 | 11795018 | 0.9975931779785554 | 48 | Illumina | SE50 unstranded | SRR3162019 | leaf | drought | na | greenhouse | na | na | both | ENA |
| Desiree | SRR3162023 | 18275400 | 49 | 18229735 | 0.9975012858815676 | 47.8 | Illumina | SE50 unstranded | SRR3162023 | leaf | control | na | field | na | na | both | ENA |
| Desiree | SRR3162027 | 19163175 | 49 | 19116224 | 0.997549936270999 | 47.9 | Illumina | SE50 unstranded | SRR3162027 | leaf | drought | na | field | na | na | both | ENA |
| Desiree | SRR3162031 | 20086368 | 49 | 20015876 | 0.9964905551864827 | 47.5 | Illumina | SE50 unstranded | SRR3162031 | leaf | control | na | field | na | na | both | ENA |
| Desiree | SRR3162035 | 19487715 | 49 | 19422314 | 0.9966439882767169 | 47.5 | Illumina | SE50 unstranded | SRR3162035 | leaf | drought | na | field | na | na | both | ENA |
| Desiree | SRR4125238 | 10635534 | 101 | 10549062 | 0.991869519668688 | 95.1 | Illumina | SE100 unstranded | SRR4125238 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125239 | 8283180 | 101 | 8220010 | 0.9923737018874393 | 95.1 | Illumina | SE100 unstranded | SRR4125239 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125240 | 8043687 | 101 | 7977558 | 0.9917787701087822 | 94.8 | Illumina | SE100 unstranded | SRR4125240 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125241 | 7944852 | 101 | 7878199 | 0.99161054227316 | 94.4 | Illumina | SE100 unstranded | SRR4125241 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125242 | 6271920 | 101 | 6123998 | 0.976415196622406 | 86.8 | Illumina | SE100 unstranded | SRR4125242 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125243 | 9980929 | 101 | 9536006 | 0.9554226866056256 | 84.4 | Illumina | SE100 unstranded | SRR4125243 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125244 | 9661094 | 101 | 9534596 | 0.9869064517952107 | 93.4 | Illumina | SE100 unstranded | SRR4125244 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125245 | 10087171 | 101 | 9997955 | 0.9911554984048551 | 95.2 | Illumina | SE100 unstranded | SRR4125245 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125246 | 9248282 | 101 | 9140995 | 0.9883992508013921 | 94.5 | Illumina | SE100 unstranded | SRR4125246 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125247 | 4256250 | 101 | 4249828 | 0.9984911600587372 | 98.2 | Illumina | SE100 unstranded | SRR4125247 | seedlings | na | na | na | na | na | both | ENA |
| Desiree | SRR4125248 | 5972182 | 101 | 5942451 | 0.9950217525185937 | 98.1 | Illumina | SE100 unstranded | SRR4125248 | root | na | na | na | na | na | both | ENA |
| Desiree | SRR4125249 | 5193719 | 101 | 5176844 | 0.9967508831340317 | 98.1 | Illumina | SE100 unstranded | SRR4125249 | root | na | na | na | na | na | both | ENA |
| Desiree | SRR4125250 | 6644676 | 101 | 6617306 | 0.9958809127788925 | 97.8 | Illumina | SE100 unstranded | SRR4125250 | root | na | na | na | na | na | both | ENA |
| Desiree | SRR4125251 | 5219511 | 101 | 5207958 | 0.9977865742595428 | 98.1 | Illumina | SE100 unstranded | SRR4125251 | root | na | na | na | na | na | both | ENA |
| Desiree | SRR4125252 | 3881450 | 101 | 3871776 | 0.9975076324569426 | 98 | Illumina | SE100 unstranded | SRR4125252 | root | na | na | na | na | na | both | ENA |
| Desiree | ERR305632_1(paired) | 52870782 | 89.2 | 52476427 | 0.9925411543941226 | 86.1 | Illumina | PE90 unstranded | ERR305632 | leaf | Phytophthora_infestans | 1 | na | na | fr | both | ENA |
| Desiree | ERR305632_1(orphans) | 1575 | 78 | 1459 | 0.9263492063492064 | 51.6 | Illumina | PE90 unstranded | ERR305632 | leaf | Phytophthora_infestans | 1 | na | na | fr | both | ENA |
| Desiree | 17_4_cut | 7515886 | 48.9 | 5042977 | 0.6709757173006615 | 39.2 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| Desiree | 17_2_cut | 9885885 | 49.3 | 7265120 | 0.7348982918575322 | 36.9 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| Desiree | 17_3_cut | 20884043 | 48.9 | 12069307 | 0.5779200416317856 | 35.9 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| Desiree | 17_1_cut | 8959293 | 49.2 | 6973672 | 0.7783730256394115 | 37.6 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| Desiree | 18_1_cut | 6442198 | 48.8 | 5014109 | 0.7783227091126351 | 36.9 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| Desiree | 18_2_cut | 7063576 | 48.8 | 5201348 | 0.7363618654347316 | 36.3 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| Desiree | 18_3_cut | 37397073 | 48.6 | 21342318 | 0.5706948776445686 | 35.6 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| Desiree | 22_1_cut | 10701303 | 48.8 | 7999325 | 0.7475094388038541 | 36.2 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | stem | na | na | growth chamber | na | na | both | NIB |
| Desiree | 22_2_cut | 45128099 | 48.5 | 26108317 | 0.5785379304366444 | 35.2 | SOLiD | SE50 unstranded | SRR10065428, SRR10065429 | stem | na | na | growth chamber | na | na | both | NIB |
| PW363 | PW363Ry-_l1 | 52609184 | 90 | 52609184 | 1 | 89.9 | Illumina | DSN PE90 unstranded | SRR10070123, SRR10070123 | leaf | PVY | 3 | growth chamber | na | fr | both | NIB |
| PW365 | PW363Ry+_l1 | 51732846 | 90 | 51732846 | 1 | 89.9 | Illumina | DSN PE90 unstranded | SRR10070123, SRR10070123 | leaf | PVY | 3 | growth chamber | na | fr | both | NIB |
| PW363 | 13_1_cut | 7403065 | 49.6 | 5684770 | 0.7679 | 37.7 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 13_2_cut | 8302545 | 49.7 | 5878593 | 0.708 | 36.9 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 13_3_cut | 19679423 | 49.6 | 10220080 | 0.5193 | 35.1 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 14_1_cut | 6583304 | 49.5 | 5270166 | 0.8005 | 37.7 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| PW363 | 14_2_cut | 7159218 | 49.6 | 5495364 | 0.7676 | 37.1 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| PW363 | 14_3_cut | 34957041 | 49.4 | 21283089 | 0.6088 | 35.9 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| PW363 | 15_1_cut | 4861705 | 48.7 | 3097549 | 0.6371 | 37.3 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 15_2_cut | 5953336 | 48.9 | 3219276 | 0.5408 | 36.6 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 15_3_cut | 44272685 | 48.1 | 26434203 | 0.5971 | 35.2 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | mock | 3 | growth chamber | na | na | both | NIB |
| PW363 | 16_1_cut | 7142875 | 49.6 | 5438028 | 0.7613 | 37.4 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| PW363 | 16_2_cut | 29588327 | 49.6 | 17198202 | 0.5812 | 36.1 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| PW363 | 16_3_cut | 3760155 | 49.3 | 2267251 | 0.603 | 38.6 | SOLiD | SE50 unstranded | SRR10065430 - SRR10065433 | leaf | PVY | 3 | growth chamber | na | na | both | NIB |
| Rywal | SH086_S1 | 70623184 | 100.6 | 69150583 | 0.9791 | 98.4 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH087_S2 | 59762572 | 100.6 | 58848024 | 0.9847 | 98.8 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH088_S3 | 60927912 | 100.6 | 60203744 | 0.9881 | 99.1 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH089_S4 | 47025982 | 100.6 | 46333721 | 0.9853 | 98.9 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH090_S5 | 53828334 | 100.6 | 52714208 | 0.9793 | 98.6 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH091_S6 | 66562628 | 100.6 | 65276650 | 0.9807 | 98.5 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene | fr | reverse | NIB |
| Rywal | SH098_S7 | 63936006 | 100.6 | 62702382 | 0.9807 | 98.5 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
| Rywal | SH099_S8 | 52719800 | 100.6 | 51787800 | 0.9823 | 97.7 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
| Rywal | SH100_S9 | 54565282 | 100.6 | 53772059 | 0.9855 | 98.9 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | mock | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
| Rywal | SH101_S10 | 60884296 | 100.6 | 60074998 | 0.9867 | 99 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
| Rywal | SH102_S11 | 61619136 | 100.6 | 60584841 | 0.9832 | 98.7 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
| Rywal | SH103_S12 | 57780944 | 100.6 | 56323961 | 0.9748 | 98 | Illumina | PE100 strand-specific | SRX6801457 - SRX6801468 | leaf | PVY | 3 | growth chamber | NahG transgene; Pti5 silencing hairpin | fr | reverse | NIB |
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| # PacBio Iso-Seq dataset | ||||||||||||||
| # processed using Iso-Seq 3 and Cupcake ToFU | ||||||||||||||
| Cultivar | SampleID | Number of reads | Avg.length | Sequencing technology | Library type | SRA_ID | Tissue | Inoculation/infestation/treatment | Days post inoculation/infestation/treatment | Plants growth conditions | Vectors or transgenic elements present | Sequencing read length | Read strandness | Data Source |
| Rywal | Rywal_IsoSeq_S1 | 28209 | 2164 | PacBio | Iso-Seq | SRR8281993 - SRR8282000 | leaf | mock | 3 | growth chamber | na | full-length transcripts | forward | NIB |
| Rywal | Rywal_IsoSeq_S2 | 28576 | 2172 | PacBio | Iso-Seq | SRR8282001 - SRR8282008 | leaf | PVY | 3 | growth chamber | na | full-length transcripts | forward | NIB |
