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
A30 F2 I2 R1 9 9.7 725596 89.2% 647231 133.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 3,004,348 G→A H373H (CAC→CAT)  PP_2623 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,004,3480GA100.0% 14.3 / NA 6H373H (CAC→CAT) PP_2623hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (4/2);  total (4/2)

TGTAGTGGGCGAGCCGGTTGACGATGAACAGGTAGGGCAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAGTGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCGCTGTCTTTACGCATGGTCAGGGCGATGA  >  NC_002947/3004251‑3004424
                                                                                                 |                                                                            
tGTAGTGGGCGAGCCGGTTGACGATGAACAGGTAGGGCAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAAcgc                                        >  1:131099/1‑136 (MQ=255)
        gCGAGCCGGTTGACGATGAACAGGTAGGGCAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGt                                >  1:174557/1‑136 (MQ=255)
          gAGCCGGTTGACGATGAACAGGTAGGGCAACTGGGTACCCAGCTTGTAGATGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGTGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCg                              >  1:354849/1‑136 (MQ=255)
                                     cAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCGCTGTCTTTACGCATGGTCAGGGCg      <  1:225770/133‑1 (MQ=255)
                                     cAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCGCTGTCTTTACGCATGGTCAGGGCg      >  2:225770/1‑133 (MQ=255)
                                      aaCTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAATGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCGCTGTCTTTACGCATGGTCAGGGCGATGa  <  2:161783/136‑1 (MQ=255)
                                                                                                 |                                                                            
TGTAGTGGGCGAGCCGGTTGACGATGAACAGGTAGGGCAACTGGGTACCCAGCTTGTAGTTGGTCTGTGCCTGAAGCCCCTCAGGGGTTTTCGGGAAGTGCTTGGGCTTTTGTACCGAGTTGGCGGAGAAGAACGCGGCGTTGTCGCTGTCTTTACGCATGGTCAGGGCGATGA  >  NC_002947/3004251‑3004424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A