Skip to main content
Fig. 4 | BMC Genomics

Fig. 4

From: Analysis of structural variation among inbred mouse strains

Fig. 4

Short-read (SR) sequence analysis has a very limited ability to identify SV present in the genome of inbred strains even when the coordinates for the SV are known. SV were identified by de novo assembly of BTBR LR genomic sequence. These results were compared with the SVs that were identified by analysis of SR BTBR genomic sequence. (A) Evaluation of the SVs identified (left panel) and genotyping calls (right panel) by the vg program are displayed by chromosome. For SV calling, 88.3% of known SVs (True Positive, TP) were correctly identified by BTBR SR genomic sequence analysis; there were no False Positive (FP) events; and only 11.6% (False Negatives, FN) of the known SV were missed using the SR sequence. However, only 29% of the known SV were correctly genotyped as homozygous by the SR analysis. (B-D) SR alignments for three heterozygous SV were visualized using the integrative genomics viewer. The deletions shown in these 3 examples are homozygous SVs present in BTBR, which were inferred from the de novo assembly of the LR BTBR genomic sequence. However, there are SR sequence segments that align with sequences within the deleted region. The repeat masker at the top of each image shows the locations of repeats and low complexity sequence regions, which are the sites that improperly align with some SR segments

Back to article page