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