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 2,331,109 A→G 47.8% intergenic (‑14/+416) 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
*minE2,331,1090AG47.8% 2.7 / 100.7 111intergenic (‑14/+416)sodA/fdhDsuperoxide dismutase, Mn/formate dehydrogenase formation protein
Reads supporting (aligned to +/- strand):  ref base A (37/21);  new base G (19/34);  total (56/55)
Fisher's exact test for biased strand distribution p-value = 4.35e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

Only 100 of 111 total aligned reads displayed.

CCAGGGCATCGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGTTAATTAAATGATA  >  minE/2331050‑2331173
                                                           |                                                                
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:3380704/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1541837/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1830863/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1856131/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1459718/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1458989/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:3227788/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:3340090/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:1204072/69‑1 (MQ=255)
ccAGGGCATCGTAAGCATACGGCAGGGATGGCAAGGTATAGCTCATATTCATCTCCAGTATTGTCGggc                                                         <  1:649454/69‑1 (MQ=255)
     gCATCGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCg                                                    >  1:1196369/1‑69 (MQ=255)
     gCATCGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCg                                                    >  1:2842481/1‑69 (MQ=255)
     gCATCGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCg                                                    >  1:2395585/1‑69 (MQ=255)
         cGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGAtt                                                 >  1:1226733/1‑68 (MQ=255)
         cGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGAtt                                                 >  1:348777/1‑68 (MQ=255)
         cGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGAtt                                                 >  1:540/1‑68 (MQ=255)
         cGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGAtt                                                 >  1:1130239/1‑68 (MQ=255)
         cGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGAtt                                                 >  1:1459902/1‑68 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:958704/1‑67 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:568059/1‑67 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:610083/1‑67 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:694496/1‑67 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:1320548/1‑67 (MQ=255)
             aGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGtt                                              >  1:1541760/1‑67 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTTATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:3125240/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTTATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:3121496/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:164465/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:2939503/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:3357256/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:2164331/68‑1 (MQ=255)
               cATACGGCAGGGATGGCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAAt                                           <  1:2089206/68‑1 (MQ=255)
                  aCGGCAGGGATGGCAGGGTGTAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:2320596/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:1593046/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:3269320/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:3253098/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:69686/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:740323/1‑69 (MQ=255)
                  aCGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCcg                                       >  1:956454/1‑69 (MQ=255)
                          gATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCa                               >  1:3395448/1‑69 (MQ=255)
                           aTGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAg                              >  1:1945548/1‑69 (MQ=255)
                              gCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTg                           >  1:1846709/1‑69 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:3212142/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:3159102/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1323184/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1175716/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:3053844/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:3000516/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:593446/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:605339/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:3297686/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1339675/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:283375/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1092785/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:705194/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1865695/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:2502383/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1012618/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:2599105/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1846738/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:2108222/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:184761/56‑1 (MQ=255)
                              gCAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGAGTGTTAATGcc                                        <  1:3381154/56‑1 (MQ=255)
                               cAGGGTATAACTCATATTCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGcc                                        <  1:1307220/55‑1 (MQ=255)
                                  ggTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTc                       >  1:649827/1‑69 (MQ=255)
                                  ggTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTc                       >  1:1504784/1‑69 (MQ=255)
                                   gTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTc                       >  1:750342/1‑68 (MQ=255)
                                     attgCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCAt                     >  1:2191155/4‑68 (MQ=255)
                                     ataGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCAt                     >  1:224529/1‑68 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:3397793/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:411437/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:579854/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:2544579/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:2288326/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:1956461/69‑1 (MQ=255)
                                           cATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGt               >  1:2029223/1‑68 (MQ=255)
                                            atatTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtt              <  1:1602667/68‑1 (MQ=255)
                                               ttCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaat           >  1:2643706/1‑68 (MQ=255)
                                               ttCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaat           >  1:422174/1‑68 (MQ=255)
                                               ttCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGtta             >  1:2954910/1‑66 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCATTTGGTTCATTATAGttaatta         >  1:3290621/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATtat                  >  1:1356960/1‑60 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1027405/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:595580/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:837608/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2962697/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1162952/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1266022/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2827542/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2521177/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2370758/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2356625/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:2047060/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1804683/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1792726/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1784226/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1696355/1‑69 (MQ=255)
                                                tCATCTCCAGTGTTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGttaatta         >  1:1675407/1‑69 (MQ=255)
                                                       cAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGc                                <  1:1009380/39‑1 (MQ=255)
                                                       cAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGTTAATTAAATGata  >  1:1565088/1‑69 (MQ=255)
                                                         gTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGTTAATTAAATGa    <  1:898277/65‑1 (MQ=255)
                                                           |                                                                
CCAGGGCATCGTAAGCATACGGCAGGGATGGCAGGGTATAGCTCATATTCATCTCCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCATTATAGTTAATTAAATGATA  >  minE/2331050‑2331173

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