Figure 2

Mapping of paired-end reads. Results of mapping 3 kb 454 paired-end reads with both ends longer than 50 nt onto the Daucus carota mitochondrial genome. Green segments in the ideogram (outer circle) indicate sequences similar to the Daucus carota plastid genome; R1-R4 in the ideogram highlight large repeat regions; letters A, B, C, D, E indicate single copy regions; blue lines and shading indicate perfect and imperfect repeat sequences; green lines indicate reads that aligned at least once within a range of 1000 and 5000 nt of each other and were considered in agreement with the assembly; red lines indicate reads that mapped outside of this range (1000 to 5000 nt) and that were considered in disagreement with the assembly. Reads in disagreement with assembly were identified as reads that mapped within repeat regions (example 1, 2 connection, white numbers) or within mitochondrial-plastid similar regions that mapped within the expected range into the plastid genome and outside of the range into the mitochondrial genome (example 3, 4, 5 connections).