Table S2.

Summary statistics of RNA-sequencing read alignment and SNP calling for the collection of Bgh isolates against isolate DH14

IsolateMaterialSequencing modeFragments sequencedAligned to DH14 genomeNo. of SNPs, total*No. of SNPs, after filtering
16 h48 hTotal16 h48 hTotal
NCIWhole leafPaired-end50,154,75351,426,484101,581,237304,804162,771467,57521,2938,246
63.5Whole leafPaired-end51,404,04651,575,361102,979,407604,5193,583,8774,188,39659,30326,495
CC1Whole leafPaired-end50,976,43151,163,669102,140,100314,8331,453,0471,767,88040,19018,061
CC66Whole leafPaired-end55,775,61452,225,048108,000,662143,4473,754,3283,897,77551,03521,341
CC88Whole leafPaired-end55,054,23050,669,586105,723,816181,650317,459499,10920,6508,008
CC107Whole leafPaired-end50,013,99048,674,52798,688,517190,9321,323,2611,514,19331,20213,832
CC52Whole leafPaired-end52,361,33857,025,784109,387,122188,006377,544565,55022,6957,613
CC148Whole leafPaired-end49,641,97156,570,523106,212,494157,735812,124969,85928,1179,906
A6Whole leafPaired-end50,793,00939,024,79289,817,8012,584,2544,184,0266,768,28078,61942,621
K1Whole leafSingle-end89,271,08379,327,402168,598,485845,2332,156,5003,001,73342,58313,653
ArtEpidermal peelPaired-end13,366,5059,982,86523,349,3706,130,3741,969,5028,099,876106,32649,392
AbyEpidermal peelPaired-end9,859,81110,671,38420,531,1951,570,3781,159,9112,730,28968,31824,353
B103Epidermal peelPaired-end9,848,0849,967,04119,815,1252,470,3471,488,3193,958,66671,32426,809
WillEpidermal peelPaired-end12,018,6569,907,61421,926,2701,914,3233,204,7415,119,06485,49737,039
OU14Epidermal peelPaired-end10,515,80310,744,04321,259,8464,070,9524,520,5918,591,543105,14750,154
RACE1Epidermal peelPaired-end10,588,50510,976,27521,564,7802,936,5805,693,3008,629,880179,08689,653
  • Leaves of the barley cultivar Pallas were inoculated with the different Bgh isolates and harvested 16 and 48 h after inoculation. For the first set of samples, RNA was isolated from whole leaves, whereas in the later samples RNA was isolated from epidermal peels to enrich for fungal RNA. Samples were subjected to Illumina paired-end or single-end sequencing. For single-end data, each fragment is represented by one read (fragments = reads), whereas for paired-end data, each fragment is represented by a pair of reads. RNA-sequencing statistics in this table and further expression analyses were based on the count of aligned fragment (i.e., for paired-end data each mapped read-pair is counted once, independent of whether one or both reads in the pair were mapped). RNA-sequencing reads were aligned to the Bgh isolate DH14 reference genome (, and all reads that aligned with MAPQ ≥ 10 were retained for further analysis.

  • * The depicted total SNP numbers were derived from the RNA-seq alignment to the DH14 genome by running the samtools mpileup function individually for each isolate.

  • To remove potentially unreliable SNP calls, the individual SNP sets were subsequently filtered, thereby excluding all calls for which at least one of the following criteria was met: (i) sequencing coverage < 3 reads; (ii) alternate allele supported by <50% of the mapped reads; (iii) SNP calling quality score < 50; (iv) genotype quality score < 10; or (v) significant strand (P > 1e−10) or tail distance (P > 1e−5) bias was detected.