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
A2 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,004,302 G→A 25.0% S483F (TCT→TTT)  hybC ← hydrogenase 2, large subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,004,3020GA25.0% 49.6 / 14.4 28S483F (TCT→TTT) hybChydrogenase 2, large subunit
Reads supporting (aligned to +/- strand):  ref base G (12/9);  new base A (4/3);  total (16/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

TTCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGC  >  minE/2004236‑2004370
                                                                  |                                                                    
ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                  <  1:291730/71‑1 (MQ=255)
  ccAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                  <  1:310049/69‑1 (MQ=255)
    aGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGGCTTTAATAACCATCCAGTGAGAGAGCATa                                                              <  1:378942/71‑1 (MQ=255)
        tGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTgagag                                                                    >  1:1278399/1‑61 (MQ=255)
        tGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTgagag                                                                    >  1:991405/1‑61 (MQ=255)
        tGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTgagag                                                                    >  1:70564/1‑61 (MQ=255)
          aTGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAAAGAGCATACcgcgc                                                        <  1:320689/71‑1 (MQ=255)
          aTGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAAAGAGCATACcgcgc                                                        <  1:179488/71‑1 (MQ=255)
             gAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTgaga                                                                     >  1:1129326/1‑55 (MQ=255)
                  acCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTc                                                >  1:392038/1‑71 (MQ=255)
                  acCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAAAGAGCATACCGCGCGGCGCTTc                                                >  1:409926/1‑71 (MQ=255)
                      ccTGGTAGTTGCTGATTATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAgg                                            <  1:853751/71‑1 (MQ=255)
                      ccTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAgg                                            <  1:1713843/71‑1 (MQ=255)
                       cTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGa                                           <  1:1801625/71‑1 (MQ=255)
                          gTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTgag                                                                      >  1:241267/1‑41 (MQ=255)
                          gTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGc                                        >  1:671073/1‑71 (MQ=255)
                                gCTGATGATACCGTCTTTAATAACCATCCAGTgaaag                                                                    >  1:319618/1‑37 (MQ=255)
                                  tgatgaTACCGTCTTTAATAACCATCCAGTGAGAGAGCa                                                                <  1:588624/39‑1 (MQ=255)
                                    atgatACCGTCTTTAATAACCATCCAGTGAGAGAGCa                                                                >  1:1465584/1‑37 (MQ=255)
                                    atgatACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCttt                              >  1:2042825/1‑71 (MQ=255)
                                    atgatACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCttt                              >  1:410126/1‑71 (MQ=255)
                                    atgatACCGTCTTTAATAACCATCCAGTGAGAGAGCATACAGCGCGGCGCTTCGAGGAAGCCAACACCtt                               >  1:908180/1‑70 (MQ=255)
                                             tCTTTAATAACCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCAcc                     <  1:1106348/71‑1 (MQ=255)
                                               tttAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCg                   >  1:1837116/1‑71 (MQ=255)
                                               tttAATAACCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCg                   >  1:2109370/1‑71 (MQ=255)
                                                 taataaCCATCCAGTGAGAGAGAATACCGCGCGGCGCTTCGAGGaa                                          >  1:908390/1‑46 (MQ=255)
                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGgcgc                                                   >  1:1176605/1‑37 (MQ=255)
                                                   ataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGc               <  1:23013/71‑1 (MQ=255)
                                                    taaCCATCCAGTGAGAGAGCATACCGCGCGCCGCTTCGAGGaa                                          <  1:1404484/43‑1 (MQ=255)
                                                      aCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCg             >  1:2102265/1‑70 (MQ=255)
                                                      aCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCg             >  1:585652/1‑70 (MQ=255)
                                                      aCCATCCAGTGAAACAGCATACCGCGCGCCGCTTCGAGGAAGCCAACACCTTTGAATTCAcc                     >  1:281358/1‑62 (MQ=255)
                                                         aTCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGaa          >  1:1479800/1‑70 (MQ=255)
                                                            cAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGt       >  1:991433/1‑70 (MQ=255)
                                                               tGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                           <  1:1788525/47‑1 (MQ=255)
                                                               tGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                           <  1:1626321/47‑1 (MQ=255)
                                                                gagagaGCATACCGCGCTGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGc  >  1:692236/1‑71 (MQ=255)
                                                                 agagagCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                           >  1:334242/1‑45 (MQ=255)
                                                                 agagagCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                           >  1:239648/1‑45 (MQ=255)
                                                                  |                                                                    
TTCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGC  >  minE/2004236‑2004370

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A