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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,664,496 T→A 52.2% V242V (GTA→GTT)  guaA ← GMP synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,664,4960TA52.2% 5.0 / 110.3 92V242V (GTA→GTT) guaAGMP synthetase
Reads supporting (aligned to +/- strand):  ref base T (19/25);  new base A (12/36);  total (31/61)
Fisher's exact test for biased strand distribution p-value = 7.96e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-01

GTTGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTCGCGGA  >  minE/1664436‑1664560
                                                            |                                                                
gTTGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACggagga                                                          <  1:483521/69‑1 (MQ=255)
gTTGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACggagga                                                          <  1:2628866/69‑1 (MQ=255)
gTTGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACggagga                                                          <  1:1545612/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGGGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1077362/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2109860/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:250994/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2225785/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:223283/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2352706/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2671762/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2831358/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2896036/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2903507/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2904070/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2907643/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:3166206/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:688480/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:770391/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:865315/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1390615/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1957960/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1426873/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1167343/69‑1 (MQ=255)
  tGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:1898871/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:3087100/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:614752/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:1770900/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:2850513/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:84720/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:2271779/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:2224097/69‑1 (MQ=255)
   gTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATc                                                       <  1:2031328/69‑1 (MQ=255)
            tACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCAcacc                                                 >  1:3086760/1‑66 (MQ=255)
            tACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCAcacc                                                 >  1:2135595/1‑66 (MQ=255)
             aCGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACAccacca                                             <  1:886519/69‑1 (MQ=255)
             aCGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACAccacca                                             <  1:962511/69‑1 (MQ=255)
             aCGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACAccacca                                             <  1:1728454/69‑1 (MQ=255)
             aCGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACAccacca                                             <  1:2403898/69‑1 (MQ=255)
             aCGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACAccacca                                             <  1:981703/69‑1 (MQ=255)
                         tttttACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGATAGGCCGAgg                                 >  1:392890/1‑69 (MQ=255)
                         tttttACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAgg                                 >  1:2450413/1‑69 (MQ=255)
                         tttttACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAgg                                 >  1:2888129/1‑69 (MQ=255)
                         tttttACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAgg                                 >  1:843684/1‑69 (MQ=255)
                             tACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATg                              <  1:1945038/68‑1 (MQ=255)
                             tACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATg                              <  1:3308472/68‑1 (MQ=255)
                             tACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATg                              <  1:3251797/68‑1 (MQ=255)
                             tACCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAAt                                                        <  1:2035684/42‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGa                             <  1:852185/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCTACCAGAGAGGCCGAGGATGa                             <  1:2329940/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2999162/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:3009534/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2130448/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:89895/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:1356068/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2306919/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:368756/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:1785628/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2545695/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:1075695/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAACAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2483128/68‑1 (MQ=255)
                              aCCGATAGCGCGGTGCAAAAGCATTGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:3166251/68‑1 (MQ=255)
                                                  gcaTTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCt        >  1:2483079/1‑69 (MQ=255)
                                                      tGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTcgcg    <  1:3172429/69‑1 (MQ=255)
                                                      tGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTcgcg    <  1:626416/69‑1 (MQ=255)
                                                      tGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTcgcg    <  1:2845973/69‑1 (MQ=255)
                                                      tGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTcgcg    <  1:2001344/69‑1 (MQ=255)
                                                      tGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTcgcg    <  1:2181118/69‑1 (MQ=255)
                                                      tGCGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGa                             <  1:2349616/44‑1 (MQ=38)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:314260/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:207481/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:1990306/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:2182260/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:1686081/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:2238589/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:2985053/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:2412355/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGAt                               >  1:118422/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTCGCgg   >  1:2802559/1‑69 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCACAAGAGAGGCCGAGGAt                               >  1:751400/1‑41 (MQ=255)
                                                       gCGGTTACGGAGGAATCCACACCA‑CAGAGAGGCCGAGGa                                >  1:2257580/1‑39 (MQ=38)
                                                        cGGTAACGGAGGACTCCACGCCACCAGAGCGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCgg   >  1:2295416/1‑68 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGcc                >  1:1225185/1‑55 (MQ=39)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCgg   >  1:1449993/1‑68 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:2490042/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:79854/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:134153/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:2775751/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:2788829/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:2834563/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:2859770/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCCACTTGCTCGCGGa  >  1:1430416/1‑69 (MQ=255)
                                                        cGGTAACGGAGGAATCCACGCCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCAACTTGCTCGCGGa  >  1:3177291/1‑69 (MQ=255)
                                                            |                                                                
GTTGTCGACGAATACGCAAGTCAGGTTTTTACCGATAGCGCGGTGCAGCAGCATTGCGGTTACGGAGGAATCCACACCACCAGAGAGGCCGAGGATGACTTTATCGTCGCCTACCTGCTCGCGGA  >  minE/1664436‑1664560

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