Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F250 I1 R1 466 525.0 9216842 90.5% 8341242 150.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGCAGAAGCATAGATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTCAGGTGCGCCAATTTATATTGTAGCATATCAGGAAGGATTAGGCTATGTCAAATAAAAAATCAAAATATTGAAATACAAATATTAGTAAATTTCTATATTTTAAAA  >  CP043523/1868331‑1868484
           |                                                                                                                                              
TGCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaata     <  SRR13214403.1539439/150‑93 (MQ=40)
TGCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaata     <  SRR13214403.1539640/150‑93 (MQ=40)
TGCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaata     <  SRR13214403.570267/150‑93 (MQ=40)
 GCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataa    <  SRR13214403.2463866/150‑94 (MQ=41)
 GCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataa    <  SRR13214403.2466229/150‑94 (MQ=41)
 GCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataa    >  SRR13214403.3005362/1‑57 (MQ=41)
 GCAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataa    >  SRR13214403.941536/1‑57 (MQ=41)
  CAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataat   <  SRR13214403.2593450/150‑95 (MQ=41)
  CAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataat   >  SRR13214403.2894609/1‑56 (MQ=41)
  CAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataat   <  SRR13214403.3685572/150‑95 (MQ=41)
  CAGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataat   <  SRR13214403.4290120/150‑95 (MQ=41)
   AGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataatg  <  SRR13214403.1979504/150‑96 (MQ=42)
   AGAAGCAT‑TATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTAAGGTACGCCActaaaaagtataccataaaaagggaatagatatgttcgtagtaggagatatccaattatcaagaaaactccaattttttggaaagttaaataatg  >  SRR13214403.947170/1‑55 (MQ=42)
           |                                                                                                                                              
TGCAGAAGCATAGATCTCACCCCCTCCCTAAGGCATTTCTGCATTGGTCAGGTGCGCCAATTTATATTGTAGCATATCAGGAAGGATTAGGCTATGTCAAATAAAAAATCAAAATATTGAAATACAAATATTAGTAAATTTCTATATTTTAAAA  >  CP043523/1868331‑1868484

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑