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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 286,800 T→C 18.7% P302P (CCT→CCC)  clpX → ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE286,8000TC18.7% 149.8 / 27.9 67P302P (CCT→CCC) clpXATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
Reads supporting (aligned to +/- strand):  ref base T (23/31);  new base C (7/5);  total (30/37)
Fisher's exact test for biased strand distribution p-value = 3.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATT  >  minE/286733‑286863
                                                                   |                                                               
aagcaagcGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCCGa                                                               >  1:2577210/1‑70 (MQ=255)
    aagcGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                                          >  1:3512077/1‑71 (MQ=255)
        gAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTg                                                       >  1:3133336/1‑70 (MQ=255)
        gAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTg                                                       >  1:2121810/1‑70 (MQ=255)
           ggCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCCGAGTTTAt                                                         <  1:3577366/65‑1 (MQ=255)
             cGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGtt                                                            <  1:692585/60‑1 (MQ=255)
             cGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGtt                                                            <  1:428705/60‑1 (MQ=255)
             cGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGtt                                                            <  1:2685532/60‑1 (MQ=255)
               aGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                                          >  1:1130704/1‑60 (MQ=255)
               aGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                                          >  1:3842965/1‑60 (MQ=255)
               aGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                                          >  1:1496440/1‑60 (MQ=255)
               aGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                                          >  1:3936953/1‑60 (MQ=255)
                 ctgctgGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGcc                                             <  1:2509856/71‑1 (MQ=255)
                   gctgGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGgtcgtc                                                 >  1:3306787/1‑65 (MQ=255)
                   gctgGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg                                           >  1:3100407/1‑71 (MQ=255)
                       gcgcAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGtt                                         <  1:1666780/69‑1 (MQ=255)
                       gcgcAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGtt                                         <  1:152581/69‑1 (MQ=255)
                       gcgcAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGtt                                         <  1:2749353/69‑1 (MQ=255)
                         gcAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCg                                     >  1:405635/1‑71 (MQ=255)
                            ggTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGtt                                                            <  1:2982657/45‑1 (MQ=255)
                             gTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:2850532/47‑1 (MQ=255)
                             gTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:2602666/47‑1 (MQ=255)
                             gTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:2944823/47‑1 (MQ=255)
                             gTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:2176325/47‑1 (MQ=255)
                             gTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:1188563/47‑1 (MQ=255)
                              ttGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGtt                                                            <  1:1639139/43‑1 (MQ=255)
                               tGAGCCGGAAGATCTGATCAAGTTTAGTCTTATCCCTGAGTTTATTg                                                       >  1:2279646/1‑47 (MQ=255)
                               tGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTg                                                       >  1:908831/1‑47 (MQ=255)
                                     ggAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTAt                                                         <  1:3886029/39‑1 (MQ=255)
                                     ggAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGc                                    <  1:2723570/60‑1 (MQ=255)
                                          aTCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         <  1:2250035/66‑1 (MQ=255)
                                          aTCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         <  1:902982/66‑1 (MQ=255)
                                          aTCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         <  1:2491609/66‑1 (MQ=255)
                                          aTCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         <  1:614330/66‑1 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCTTCTGCCgg                                           <  1:1953272/47‑1 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg                                           <  1:3279216/47‑1 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg                                           <  1:429270/47‑1 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg                                           <  1:2739630/47‑1 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACt                     >  1:3973823/1‑69 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACt                     >  1:1836849/1‑69 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACt                     >  1:2737732/1‑69 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaa                           >  1:3065899/1‑63 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaa                           >  1:3245924/1‑63 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaa                           >  1:2239475/1‑63 (MQ=255)
                                           tCTGATCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaa                           >  1:2724547/1‑63 (MQ=255)
                                            cTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTTTCGCAACGTtgaatgaa                       >  1:1314479/1‑66 (MQ=255)
                                            cTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatgaa                       >  1:415978/1‑66 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCga               <  1:3338568/71‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCga               <  1:3696090/71‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCga               <  1:961351/71‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCg                <  1:1176678/70‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTg                    <  1:3422629/66‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTg                    <  1:2237013/66‑1 (MQ=255)
                                               aTCAAGTTTGGTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTg                    <  1:1102304/66‑1 (MQ=255)
                                                    gTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGaagaag          <  1:1182396/71‑1 (MQ=255)
                                                         gTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCATCGTTGAATGAACTGAGCGAAGAAGgtct      <  1:691817/70‑1 (MQ=255)
                                                         gTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGctct      <  1:617754/70‑1 (MQ=255)
                                                         gTCTTATCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGctct      <  1:3839968/70‑1 (MQ=255)
                                                         gTCTTATCCCAGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGctct      <  1:3018958/70‑1 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         >  1:3437859/1‑46 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         >  1:405543/1‑46 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         >  1:3052732/1‑46 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         >  1:2410407/1‑46 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatg                         >  1:2489607/1‑46 (MQ=255)
                                                              aTCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaa                           >  1:3084809/1‑44 (MQ=255)
                                                              aTCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGAtt  >  1:1911445/1‑69 (MQ=255)
                                                              aTCCCCGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGAtt  >  1:2218074/1‑69 (MQ=255)
                                                                   |                                                               
AAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGAAGCTCTGATT  >  minE/286733‑286863

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

GATK/CNVnator alignment

N/A