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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,331,252 A→C 78.6% 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
*minE2,331,2520AC78.6% 219.8 / 30.1 92intergenic (‑157/+273)sodA/fdhDsuperoxide dismutase, Mn/formate dehydrogenase formation protein
Reads supporting (aligned to +/- strand):  ref base A (14/6);  new base C (29/43);  total (43/49)
Fisher's exact test for biased strand distribution p-value = 2.34e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCAC  >  minE/2331186‑2331320
                                                                  |                                                                    
aTCAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCAc                                                                  >  1:625338/1‑71 (MQ=255)
aTCAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCAc                                                                  >  1:3639867/1‑71 (MQ=255)
       ccGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                              >  1:1609399/1‑68 (MQ=255)
       ccGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                              >  1:1627777/1‑68 (MQ=255)
       ccGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGc                                                           <  1:1832285/71‑1 (MQ=255)
       ccGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGc                                                           >  1:238016/1‑71 (MQ=255)
       ccGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACAACTTAATGc                                                           >  1:4120493/1‑71 (MQ=255)
          tACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                        <  1:914299/71‑1 (MQ=255)
          tACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                        <  1:2354273/71‑1 (MQ=255)
          tACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGt                                                        <  1:1878856/71‑1 (MQ=255)
             ttttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTg                                                       <  1:4142604/69‑1 (MQ=255)
             ttttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCAc                                                                  <  1:5394673/58‑1 (MQ=255)
             ttttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCAc                                                                  <  1:4657282/58‑1 (MQ=255)
             ttttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACtt                                                                <  1:332194/60‑1 (MQ=255)
              tttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                              <  1:1084040/61‑1 (MQ=255)
               ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCaa                                                                      >  1:5648226/1‑52 (MQ=255)
               ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCaa                                                                      >  1:2887715/1‑52 (MQ=255)
               ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                              >  1:3289638/1‑60 (MQ=255)
               ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTg                                                   >  1:3975255/1‑71 (MQ=255)
               ttCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTg                                                   >  1:904973/1‑71 (MQ=255)
                    aaGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAg                                               >  1:468762/1‑70 (MQ=255)
                      gggTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTa                                             >  1:3763569/1‑70 (MQ=255)
                        gTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAAt                                          >  1:4490629/1‑71 (MQ=255)
                         tATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACtt                                                                <  1:4603587/48‑1 (MQ=255)
                         tATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACt                                                                 <  1:3075121/47‑1 (MQ=255)
                         tATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACt                                                                 <  1:3692467/47‑1 (MQ=255)
                         tATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATc                                         >  1:2034377/1‑71 (MQ=255)
                          aTGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTa                                                               <  1:2146702/48‑1 (MQ=255)
                           tGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACtt                                                                <  1:833988/46‑1 (MQ=255)
                           tGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGa                                       >  1:550635/1‑71 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                        <  1:88732/52‑1 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGt                                                        <  1:3395909/52‑1 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:3481074/1‑70 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      <  1:597334/70‑1 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      <  1:2779101/70‑1 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      <  1:588385/70‑1 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCAc                                                                  >  1:5680633/1‑42 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCAc                                                                  >  1:4535801/1‑42 (MQ=255)
                             gTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTaaa                                           >  1:2705363/1‑65 (MQ=255)
                              ttttGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGa                                                      <  1:4824989/53‑1 (MQ=255)
                              ttttGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                                    >  1:1795100/1‑71 (MQ=255)
                                ttGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTaa                                                              >  1:2909005/1‑43 (MQ=255)
                                 tGCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcg                                  <  1:5537938/70‑1 (MQ=255)
                                  gCAGGAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGa                                                      <  1:1253521/49‑1 (MQ=255)
                                     tgAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGcc                                                 <  1:448367/50‑1 (MQ=39)
                                     ggAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGcc                                                 <  1:4701496/51‑1 (MQ=255)
                                     ggAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                             <  1:3841890/71‑1 (MQ=255)
                                     ggAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                             <  1:2097179/71‑1 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGa                                                      >  1:976224/1‑45 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      <  1:1464347/61‑1 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      <  1:3488160/61‑1 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:5214068/1‑61 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                             >  1:1175763/1‑70 (MQ=255)
                                      gAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                                 <  1:4937783/66‑1 (MQ=255)
                                       aaaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAg                                               >  1:2522956/1‑51 (MQ=255)
                                       aaaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                           <  1:3072336/71‑1 (MQ=255)
                                       aaaaTGACCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                           <  1:159785/71‑1 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                                 <  1:3805475/64‑1 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                                 <  1:1931042/64‑1 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                                 <  1:901316/64‑1 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAAcgg                                 <  1:1815957/64‑1 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                           >  1:2353203/1‑70 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:1481875/1‑59 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:3959613/1‑59 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:27763/1‑59 (MQ=255)
                                        aaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGAc                                      >  1:4818556/1‑59 (MQ=255)
                                         aaTGCCCGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                           >  1:148248/1‑69 (MQ=255)
                                              ccGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa                    <  1:4871065/71‑1 (MQ=255)
                                              ccGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa                    <  1:2840703/71‑1 (MQ=255)
                                               cGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa                    <  1:2957409/70‑1 (MQ=255)
                                               cGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa                    <  1:5049134/70‑1 (MQ=255)
                                               cGAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGa                    <  1:805124/70‑1 (MQ=255)
                                                gagaTGTGAAGCAAATCACCCACTTAATGCCGTGAt                                                     >  1:3792227/1‑36 (MQ=255)
                                                gagaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGaaa                  <  1:4253465/71‑1 (MQ=255)
                                                 agaTGTGAAGCAAATCACCCACTTAATGCCGTGAt                                                     <  1:5117195/35‑1 (MQ=255)
                                                 agaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGcc                                                 <  1:2277130/39‑1 (MQ=255)
                                                  gaTGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAgg                >  1:5358737/1‑71 (MQ=255)
                                                    tgtgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTa                                             <  1:448712/40‑1 (MQ=255)
                                                     gtgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTa                                             <  1:5081081/39‑1 (MQ=255)
                                                     gtgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt              >  1:5281524/1‑70 (MQ=255)
                                                      tgAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTaa            <  1:2015184/71‑1 (MQ=255)
                                                      tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTaaa                                           >  1:5082922/1‑40 (MQ=255)
                                                        aaGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc          <  1:2404480/71‑1 (MQ=255)
                                                        aaGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc          >  1:2342394/1‑71 (MQ=255)
                                                        aaGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc          <  1:257715/71‑1 (MQ=255)
                                                             aaTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCaa                           >  1:838772/1‑49 (MQ=255)
                                                             aaTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAAc                          >  1:998265/1‑50 (MQ=255)
                                                             aaTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAAc                          >  1:1510757/1‑50 (MQ=255)
                                                              aTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTa             >  1:4734805/1‑62 (MQ=255)
                                                              aTCACCCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGc    <  1:4003264/71‑1 (MQ=255)
                                                               tCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                                    >  1:4731933/1‑38 (MQ=255)
                                                               tCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                                    >  1:4509085/1‑38 (MQ=255)
                                                               tCACCCACTTAATGCCGTGATTGCCAGTAAATCGACaa                                    >  1:3381377/1‑38 (MQ=255)
                                                                cAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCAc  >  1:1094501/1‑71 (MQ=255)
                                                                 aaCCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                             <  1:5209123/43‑1 (MQ=255)
                                                                 aaCCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc                             <  1:3421951/43‑1 (MQ=255)
                                                                  |                                                                    
ATCAATGCCGTACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCAC  >  minE/2331186‑2331320

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