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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,331,252 A→C 61.1% intergenic (‑157/+273) sodA ← / ← fdhD superoxide dismutase, Mn/formate dehydrogenase formation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,331,2520AC61.1% 72.1 / 50.5 59intergenic (‑157/+273)sodA/fdhDsuperoxide dismutase, Mn/formate dehydrogenase formation protein
Reads supporting (aligned to +/- strand):  ref base A (9/14);  new base C (22/14);  total (31/28)
Fisher's exact test for biased strand distribution p-value = 1.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGA  >  minE/2331188‑2331314
                                                                |                                                              
cAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACt                                                           >  1:1891708/1‑70 (MQ=255)
 aaTGCTGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTa                                                         <  1:1821770/71‑1 (MQ=255)
 aaTGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACtt                                                          <  1:603953/70‑1 (MQ=255)
            tttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATg                                                      >  1:637332/1‑63 (MQ=255)
             ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCa                                                             >  1:1020269/1‑55 (MQ=255)
             ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                        >  1:2852444/1‑60 (MQ=255)
             ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTg                                             >  1:3720495/1‑71 (MQ=255)
              tCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAAt                                                       <  1:252489/60‑1 (MQ=255)
                  aaGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAg                                         >  1:3907905/1‑70 (MQ=255)
                  aaGGGTATGGTTTTGCAAGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAg                                         >  1:331034/1‑70 (MQ=255)
                   aGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAAt                                                       >  1:3249319/1‑55 (MQ=255)
                    gggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTa                                       >  1:988015/1‑70 (MQ=255)
                     tgTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTaaa                                     <  1:2474186/70‑1 (MQ=255)
                     ggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                  >  1:2146903/1‑58 (MQ=255)
                     ggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                  >  1:3443170/1‑58 (MQ=255)
                     ggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTaaa                                     <  1:22874/71‑1 (MQ=255)
                     ggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGc                                            >  1:908999/1‑64 (MQ=255)
                      gTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGc                                            <  1:1229334/63‑1 (MQ=255)
                      gTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGc                                            <  1:109212/63‑1 (MQ=255)
                      gTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTaa                                      <  1:2532320/69‑1 (MQ=255)
                       tATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATc                                   >  1:3582258/1‑71 (MQ=255)
                        aTGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAATTc                                   >  1:3932086/1‑70 (MQ=255)
                         tGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGa                                 >  1:467166/1‑71 (MQ=255)
                          ggTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGa                                 >  1:3679141/1‑70 (MQ=255)
                           gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                <  1:515112/70‑1 (MQ=255)
                            ttttGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                              >  1:3562784/1‑71 (MQ=255)
                            ttttGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                              <  1:3906902/71‑1 (MQ=255)
                            ttttGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGt                                                  <  1:2990256/51‑1 (MQ=255)
                             tttGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTATTGc                                                     >  1:2448259/1‑47 (MQ=255)
                              ttGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAAcg                            >  1:3711050/1‑71 (MQ=255)
                               tGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                <  1:1812039/66‑1 (MQ=255)
                                gCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                           <  1:3424222/70‑1 (MQ=255)
                                gCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                           <  1:862565/70‑1 (MQ=255)
                                  aGGAAAATGCCCGAGATGTGAAGCAAATCACCCTCTTAATGCCGTGATTGCGAGTAAATCGACAAcg                            <  1:3469139/67‑1 (MQ=255)
                                   ggAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                       <  1:3108632/71‑1 (MQ=255)
                                    gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGa                                 <  1:3287068/60‑1 (MQ=255)
                                    gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGa                                 <  1:2423263/60‑1 (MQ=255)
                                     aaaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                     >  1:3856441/1‑71 (MQ=255)
                                     aaaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                     >  1:3782967/1‑71 (MQ=255)
                                        aTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAg                  >  1:2839837/1‑71 (MQ=255)
                                        aTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAg                  <  1:2655560/71‑1 (MQ=255)
                                           cccGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcggcg                         >  1:1301340/1‑61 (MQ=255)
                                            ccGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCg               >  1:1011645/1‑70 (MQ=255)
                                             cGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAAt                                    <  1:291661/48‑1 (MQ=255)
                                              gagaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGaaa            <  1:2173629/71‑1 (MQ=255)
                                              gagaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa              >  1:1660612/1‑69 (MQ=255)
                                              gagaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa              >  1:2519403/1‑69 (MQ=255)
                                              gagaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa              >  1:885311/1‑69 (MQ=255)
                                              gagaTGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTa                                       >  1:3611225/1‑44 (MQ=255)
                                              gagaTGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGaaa            <  1:86185/71‑1 (MQ=255)
                                              gagaTGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGaaa            <  1:2412087/71‑1 (MQ=255)
                                               agaTGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                     >  1:1140024/1‑61 (MQ=255)
                                                  tgtgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt        <  1:2051632/71‑1 (MQ=255)
                                                    tgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCg                                  >  1:2616625/1‑43 (MQ=255)
                                                    tgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTaa      <  1:3516244/71‑1 (MQ=255)
                                                       aGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCg   <  1:2868067/71‑1 (MQ=255)
                                                         cAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAgg          <  1:3789370/62‑1 (MQ=255)
                                                         cAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAgg          <  1:1789007/62‑1 (MQ=255)
                                                          aaaTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGa  >  1:2359647/1‑69 (MQ=255)
                                                                |                                                              
CAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGA  >  minE/2331188‑2331314

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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