Experiment: plant=Squash; plant sample=QP3; plant location=NA
Only strains with sufficient reads to estimate fitness are shown,
but the strain fitness values are still rather noisy and may be biased towards zero.
Strains near the edge of a gene are not shown as being associated with that
gene (they are in grey).
Strains in the central 10-90% of a gene are color coded by the insertion's strand.
Usually, "+" means that the selectable marker is encoded on the forward strand,
i.e., transcribed rightward.
500 nt hofC and gspE overlap by 23 nucleotides gspE and ppdD overlap by 1 nucleotides ppdD and nadC are separated by 195 nucleotides
LU632_RS03025: hofC - protein transport protein HofC, at 617,881 to 619,080
hofC
LU632_RS03030: gspE - type II secretion system protein GspE, at 619,058 to 620,461
gspE
LU632_RS03035: ppdD - prepilin peptidase-dependent pilin, at 620,461 to 620,913
ppdD
LU632_RS03040: nadC - carboxylating nicotinate-nucleotide diphosphorylase, at 621,109 to 621,996
nadC
Position (kb) 619
620
621 Strain fitness (log2 ratio) -2
-1
0
1
2
3 at 618.092 kb on + strand, within hofC at 618.132 kb on + strand, within hofC at 618.132 kb on + strand, within hofC at 618.133 kb on - strand, within hofC at 618.135 kb on - strand, within hofC at 618.135 kb on - strand, within hofC at 618.135 kb on - strand, within hofC at 618.136 kb on + strand, within hofC at 618.136 kb on + strand, within hofC at 618.137 kb on - strand, within hofC at 618.156 kb on + strand, within hofC at 618.157 kb on - strand, within hofC at 618.223 kb on + strand, within hofC at 618.228 kb on + strand, within hofC at 618.274 kb on - strand, within hofC at 618.274 kb on - strand, within hofC at 618.274 kb on - strand, within hofC at 618.277 kb on + strand, within hofC at 618.278 kb on - strand, within hofC at 618.278 kb on - strand, within hofC at 618.348 kb on + strand, within hofC at 618.395 kb on + strand, within hofC at 618.406 kb on + strand, within hofC at 618.406 kb on + strand, within hofC at 618.407 kb on - strand, within hofC at 618.460 kb on + strand, within hofC at 618.460 kb on + strand, within hofC at 618.503 kb on + strand, within hofC at 618.503 kb on + strand, within hofC at 618.503 kb on + strand, within hofC at 618.505 kb on + strand, within hofC at 618.506 kb on - strand, within hofC at 618.527 kb on - strand, within hofC at 618.613 kb on + strand, within hofC at 618.666 kb on + strand, within hofC at 618.769 kb on - strand, within hofC at 618.864 kb on + strand, within hofC at 618.869 kb on - strand, within hofC at 618.920 kb on - strand, within hofC at 618.974 kb on - strand at 619.103 kb on + strand at 619.120 kb on + strand at 619.158 kb on - strand at 619.188 kb on - strand at 619.193 kb on + strand at 619.194 kb on - strand at 619.194 kb on - strand at 619.282 kb on - strand, within gspE at 619.504 kb on + strand, within gspE at 619.505 kb on - strand, within gspE at 619.508 kb on + strand, within gspE at 619.513 kb on + strand, within gspE at 619.513 kb on + strand, within gspE at 619.591 kb on + strand, within gspE at 619.591 kb on + strand, within gspE at 619.592 kb on - strand, within gspE at 619.595 kb on - strand, within gspE at 619.661 kb on + strand, within gspE at 619.662 kb on - strand, within gspE at 619.662 kb on - strand, within gspE at 619.714 kb on + strand, within gspE at 619.743 kb on + strand, within gspE at 619.744 kb on - strand, within gspE at 619.744 kb on - strand, within gspE at 619.744 kb on - strand, within gspE at 619.758 kb on + strand, within gspE at 619.903 kb on + strand, within gspE at 619.903 kb on + strand, within gspE at 620.008 kb on + strand, within gspE at 620.009 kb on - strand, within gspE at 620.102 kb on + strand, within gspE at 620.103 kb on - strand, within gspE at 620.105 kb on - strand, within gspE at 620.105 kb on - strand, within gspE at 620.105 kb on - strand, within gspE at 620.134 kb on + strand, within gspE at 620.159 kb on - strand, within gspE at 620.159 kb on - strand, within gspE at 620.189 kb on + strand, within gspE at 620.218 kb on + strand, within gspE at 620.295 kb on + strand, within gspE at 620.305 kb on + strand, within gspE at 620.314 kb on + strand, within gspE at 620.315 kb on - strand, within gspE at 620.324 kb on - strand at 620.342 kb on + strand at 620.342 kb on + strand at 620.343 kb on - strand at 620.392 kb on + strand at 620.428 kb on + strand at 620.428 kb on + strand at 620.429 kb on - strand at 620.559 kb on + strand, within ppdD at 620.559 kb on + strand, within ppdD at 620.560 kb on - strand, within ppdD at 620.672 kb on + strand, within ppdD at 620.673 kb on - strand, within ppdD at 620.756 kb on - strand, within ppdD at 620.767 kb on - strand, within ppdD at 620.816 kb on + strand, within ppdD at 620.817 kb on - strand, within ppdD at 620.892 kb on + strand at 620.893 kb on - strand at 620.918 kb on + strand at 620.919 kb on - strand at 621.032 kb on - strand at 621.032 kb on - strand at 621.032 kb on - strand at 621.032 kb on - strand at 621.127 kb on + strand at 621.144 kb on + strand at 621.194 kb on + strand at 621.342 kb on + strand, within nadC at 621.343 kb on - strand, within nadC at 621.455 kb on + strand, within nadC
Per-strain Table
Position Strand Gene LocusTag Fraction plant=Squash; plant sample=QP3; plant location=NA remove 618,092 + hofC LU632_RS03025 0.18 +0.5 618,132 + hofC LU632_RS03025 0.21 +0.2 618,132 + hofC LU632_RS03025 0.21 +0.0 618,133 - hofC LU632_RS03025 0.21 +0.0 618,135 - hofC LU632_RS03025 0.21 +0.0 618,135 - hofC LU632_RS03025 0.21 -0.3 618,135 - hofC LU632_RS03025 0.21 -0.1 618,136 + hofC LU632_RS03025 0.21 -0.2 618,136 + hofC LU632_RS03025 0.21 -2.0 618,137 - hofC LU632_RS03025 0.21 -1.2 618,156 + hofC LU632_RS03025 0.23 +0.7 618,157 - hofC LU632_RS03025 0.23 -1.0 618,223 + hofC LU632_RS03025 0.28 +1.1 618,228 + hofC LU632_RS03025 0.29 +0.7 618,274 - hofC LU632_RS03025 0.33 -0.6 618,274 - hofC LU632_RS03025 0.33 -1.2 618,274 - hofC LU632_RS03025 0.33 -0.7 618,277 + hofC LU632_RS03025 0.33 +1.4 618,278 - hofC LU632_RS03025 0.33 +0.0 618,278 - hofC LU632_RS03025 0.33 +0.9 618,348 + hofC LU632_RS03025 0.39 -2.5 618,395 + hofC LU632_RS03025 0.43 +1.1 618,406 + hofC LU632_RS03025 0.44 -0.7 618,406 + hofC LU632_RS03025 0.44 -0.9 618,407 - hofC LU632_RS03025 0.44 +0.1 618,460 + hofC LU632_RS03025 0.48 +0.4 618,460 + hofC LU632_RS03025 0.48 +1.2 618,503 + hofC LU632_RS03025 0.52 +3.4 618,503 + hofC LU632_RS03025 0.52 -1.2 618,503 + hofC LU632_RS03025 0.52 +0.3 618,505 + hofC LU632_RS03025 0.52 -0.1 618,506 - hofC LU632_RS03025 0.52 +0.6 618,527 - hofC LU632_RS03025 0.54 -1.5 618,613 + hofC LU632_RS03025 0.61 +2.2 618,666 + hofC LU632_RS03025 0.65 -2.2 618,769 - hofC LU632_RS03025 0.74 -0.9 618,864 + hofC LU632_RS03025 0.82 -0.4 618,869 - hofC LU632_RS03025 0.82 -0.3 618,920 - hofC LU632_RS03025 0.87 +0.1 618,974 - -0.3 619,103 + +0.2 619,120 + +1.0 619,158 - +0.7 619,188 - +2.6 619,193 + -0.7 619,194 - +1.3 619,194 - -0.4 619,282 - gspE LU632_RS03030 0.16 +0.6 619,504 + gspE LU632_RS03030 0.32 -0.8 619,505 - gspE LU632_RS03030 0.32 -0.2 619,508 + gspE LU632_RS03030 0.32 +0.3 619,513 + gspE LU632_RS03030 0.32 -0.6 619,513 + gspE LU632_RS03030 0.32 -1.0 619,591 + gspE LU632_RS03030 0.38 -0.7 619,591 + gspE LU632_RS03030 0.38 -0.4 619,592 - gspE LU632_RS03030 0.38 -0.3 619,595 - gspE LU632_RS03030 0.38 +0.6 619,661 + gspE LU632_RS03030 0.43 -1.0 619,662 - gspE LU632_RS03030 0.43 -1.3 619,662 - gspE LU632_RS03030 0.43 +2.6 619,714 + gspE LU632_RS03030 0.47 -1.4 619,743 + gspE LU632_RS03030 0.49 +0.4 619,744 - gspE LU632_RS03030 0.49 -0.1 619,744 - gspE LU632_RS03030 0.49 -0.9 619,744 - gspE LU632_RS03030 0.49 +1.3 619,758 + gspE LU632_RS03030 0.50 +0.8 619,903 + gspE LU632_RS03030 0.60 -0.8 619,903 + gspE LU632_RS03030 0.60 +0.3 620,008 + gspE LU632_RS03030 0.68 -0.4 620,009 - gspE LU632_RS03030 0.68 +0.9 620,102 + gspE LU632_RS03030 0.74 -0.0 620,103 - gspE LU632_RS03030 0.74 -1.4 620,105 - gspE LU632_RS03030 0.75 +0.6 620,105 - gspE LU632_RS03030 0.75 +0.4 620,105 - gspE LU632_RS03030 0.75 -0.0 620,134 + gspE LU632_RS03030 0.77 -0.6 620,159 - gspE LU632_RS03030 0.78 +0.5 620,159 - gspE LU632_RS03030 0.78 -0.3 620,189 + gspE LU632_RS03030 0.81 +0.2 620,218 + gspE LU632_RS03030 0.83 +0.5 620,295 + gspE LU632_RS03030 0.88 -1.4 620,305 + gspE LU632_RS03030 0.89 +0.8 620,314 + gspE LU632_RS03030 0.89 -0.5 620,315 - gspE LU632_RS03030 0.90 +0.9 620,324 - -0.6 620,342 + -0.1 620,342 + -0.5 620,343 - -1.0 620,392 + -1.4 620,428 + +0.4 620,428 + -1.2 620,429 - +3.5 620,559 + ppdD LU632_RS03035 0.22 -0.6 620,559 + ppdD LU632_RS03035 0.22 +0.1 620,560 - ppdD LU632_RS03035 0.22 +1.0 620,672 + ppdD LU632_RS03035 0.47 -0.0 620,673 - ppdD LU632_RS03035 0.47 -0.5 620,756 - ppdD LU632_RS03035 0.65 -1.0 620,767 - ppdD LU632_RS03035 0.68 -2.4 620,816 + ppdD LU632_RS03035 0.78 +0.6 620,817 - ppdD LU632_RS03035 0.79 +0.3 620,892 + -1.6 620,893 - -1.5 620,918 + -1.4 620,919 - +0.6 621,032 - +0.5 621,032 - +2.1 621,032 - +0.1 621,032 - -0.3 621,127 + -0.9 621,144 + +0.6 621,194 + -1.4 621,342 + nadC LU632_RS03040 0.26 +0.6 621,343 - nadC LU632_RS03040 0.26 +0.6 621,455 + nadC LU632_RS03040 0.39 -1.1
Or see this region's nucleotide sequence