Table of Contents
Section 0. GAEMR Summary
Figure 0.1 Cumulative Sizes
Figure 0.2 Blast Bubbles
Figure 0.3 Coverage Line Plot and GC
Table 0.1 rRNA Analysis Summary
Figure 0.4 Alignment to Reference
Section 1. Assembly Stats
Table 1.1. Basic Assembly Stats
Table 1.2. rRNA Analysis Summary
Figure 1.1. Cumulative Sizes
Section 2. Read Alignment Stats
Figure 2.1 Coverage Line Plot and GC
Figure 2.2 Scaffold GC Coverage Histogram
Table 2.1 Simple BAM Stats
Table 2.2 Sequence Coverage Stats
Table 2.3 Physical Coverage Stats
Table 2.4 Insert Size Stats
Figure 2.3 Scaffold Insert Size
Figure 2.4 Coverage Anomalies Scatter Plot
Figure 2.5 Scaffold Coverage Anomalies Cluster Length
Figure 2.6 Scaffold Coverage Anomalies Change in Coverage Scatter Plot
Figure 2.7 Scaffold Coverage Anomalies Change in Coverage Histogram
Section 3. Kmer Analysis
Table 3.1. Kmer Copy Number
Section 4. Gap End Analysis
Table 4.1. Gap End Analysis Table
Table 4.2. Gap End Simple Sequence Analysis Table
Figure 4.1. CG Sizes
Figure 4.2. CG Distinctness
Figure 4.3. CG Copy Number
Figure 4.4. CG GC
Figure 4.5. UE Distinctness
Figure 4.6. UE Copy Number
Figure 4.7. UE GC
Section 5. Reference Analysis
Figure 5.1 Alignment to Reference
Table 5.1 Scaffold Accuracy
Table 5.2 Kmer Coverage
Figure 5.2 Coverage Line Plot and GC
Figure 5.3 GC Coverage Histogram
Table 5.3 Reference Simple BAM Stats Table
Table 5.4 Reference Sequence Coverage Stat
Table 5.5 Physical Coverage Stats
Figure 5.4 Insert Size
Table 5.6 Insert Size Stats
Figure 5.5 Comparison To Reference
Figure 5.6 Coverage Anomalies Scatter Plot
Figure 5.7 Coverage Anomalies Bar Plot
Figure 5.8 Coverage Change Across Bases Scatter Plot
Figure 5.9 Coverage Change Across Bases Histogram
Section 6. Blast Analysis
Figure 6.1 Blast Bubbles
Figure 6.2 Blast Heat Map
Table 6.1 Blast Taxonomy Details
Section 7. rRNA Details
Table 7.1. rRNA Analysis Details
Section 8. Assembly Details
Table 8.1. Contig Details
Table 8.2. Scaffold Details