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 1,259,361 G→A 20.9% S521S (AGC→AGT)  torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,259,3610GA20.9% 351.9 / 79.1 172S521S (AGC→AGT) torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base G (68/68);  new base A (17/19);  total (85/87)
Fisher's exact test for biased strand distribution p-value = 8.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

Only 100 of 172 total aligned reads displayed.

ACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACGATATCTGCG  >  minE/1259293‑1259430
                                                                    |                                                                     
acGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                                     <  1:3570864/71‑1 (MQ=255)
 catCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTg                                                                    >  1:316453/3‑71 (MQ=255)
   tCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTa                                                                  <  1:579815/71‑1 (MQ=255)
   tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                                  <  1:2676923/71‑1 (MQ=255)
   tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                                  <  1:5523638/71‑1 (MQ=255)
   tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                                  <  1:832803/71‑1 (MQ=255)
     aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTaa                                                                 >  1:1025002/1‑70 (MQ=255)
     aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                                >  1:2360281/1‑71 (MQ=255)
      aaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                                >  1:4862634/1‑70 (MQ=255)
       aaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                                     >  1:4330394/1‑64 (MQ=255)
         tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                                     <  1:5148167/62‑1 (MQ=255)
           gTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCgg                                                          >  1:1723786/1‑71 (MQ=255)
           gTTACGCGCTTAAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCgg                                                          >  1:3466036/1‑71 (MQ=255)
              aCGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                                       >  1:836881/1‑71 (MQ=255)
               cgcgCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                                       <  1:498131/70‑1 (MQ=255)
                gcgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                                     <  1:1981736/71‑1 (MQ=255)
                  gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                             >  1:5050578/1‑61 (MQ=255)
                   cTTCAAATTGCGGAGCAAGAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                             <  1:4728641/60‑1 (MQ=255)
                   cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGc                                                                      <  1:3651464/51‑1 (MQ=255)
                   cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                                     >  1:5582834/1‑52 (MQ=255)
                    ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGt                                                                   <  1:937645/53‑1 (MQ=255)
                    ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                                  >  1:5549815/1‑70 (MQ=255)
                    ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                                  >  1:4572777/1‑70 (MQ=255)
                     tCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                                  >  1:856251/1‑69 (MQ=255)
                       aaaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                                     >  1:1534788/1‑64 (MQ=255)
                        aaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                             <  1:2069629/71‑1 (MQ=255)
                         aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                             <  1:5453119/70‑1 (MQ=255)
                          ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAtac                                                              >  1:1033626/1‑50 (MQ=255)
                           tGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                          >  1:2781082/1‑71 (MQ=255)
                            gCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                          <  1:5179392/70‑1 (MQ=255)
                                  cAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTc                                    >  1:3774467/1‑70 (MQ=255)
                                    aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCTTCAAGTCATTGCGCTCaaa                                 >  1:5316869/1‑71 (MQ=255)
                                    aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                          >  1:5518979/1‑62 (MQ=255)
                                    aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                                 <  1:5628727/71‑1 (MQ=255)
                                    aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                                 <  1:4148397/71‑1 (MQ=255)
                                    aCAGCCTGCTTCATCGGCACAATATGCTGGTAGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                                 >  1:4892277/1‑71 (MQ=255)
                                    aCAGCCTGCTTCATAGGCACAATATGCTGGTTGATGt                                                                   >  1:5093352/1‑37 (MQ=38)
                                     cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                              <  1:878753/57‑1 (MQ=255)
                                     cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                              <  1:195285/57‑1 (MQ=255)
                                     cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                                <  1:1167206/71‑1 (MQ=255)
                                      aGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                                >  1:4465805/1‑70 (MQ=255)
                                       gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                            >  1:909550/1‑57 (MQ=255)
                                       gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                            >  1:3182833/1‑57 (MQ=255)
                                       gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGa                              >  1:2465211/1‑71 (MQ=255)
                                        ccTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                                  <  1:320250/66‑1 (MQ=255)
                                         ttGCTTCATCGGCACCAGATGCTGATTACTGTAAt                                                                >  1:3487193/2‑35 (MQ=19)
                                         ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                          <  1:1105413/56‑1 (MQ=255)
                                         ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                          <  1:2268699/56‑1 (MQ=255)
                                         ttGCTTCATCGGCACCAGATGCTGAATACTGTAATCACCGGTCATGGTGAGATCATTACGCTCaaaag                               <  1:3971516/67‑3 (MQ=255)
                                         cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                            <  1:2590335/71‑1 (MQ=255)
                                         cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                            <  1:71537/71‑1 (MQ=255)
                                          tGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                            >  1:299908/1‑68 (MQ=255)
                                          tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgt                           >  1:2879637/1‑71 (MQ=255)
                                          tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgt                           >  1:1590814/1‑71 (MQ=255)
                                          tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCCCTCAAACGAtgt                           >  1:3636816/1‑71 (MQ=255)
                                           gCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                            >  1:4307876/1‑67 (MQ=255)
                                           gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                          >  1:5367628/1‑71 (MQ=255)
                                            cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                          <  1:2951810/70‑1 (MQ=255)
                                            cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtgg                         <  1:3553840/71‑1 (MQ=255)
                                             ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                          >  1:3875618/1‑53 (MQ=255)
                                             ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                                       >  1:2916854/1‑40 (MQ=255)
                                             ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                                <  1:1552641/63‑1 (MQ=255)
                                             ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                                <  1:4697260/63‑1 (MQ=255)
                                              tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt                        >  1:3802995/1‑70 (MQ=255)
                                              tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt                        >  1:4743670/1‑70 (MQ=255)
                                               cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                                         >  1:1386202/1‑51 (MQ=255)
                                               cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                                         >  1:1894571/1‑51 (MQ=255)
                                                aTCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagtcg                      >  1:3031055/1‑68 (MQ=255)
                                                aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt                     <  1:3427176/71‑1 (MQ=255)
                                                aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt                     <  1:1655858/71‑1 (MQ=255)
                                                aTCGGCACAATATGCTGGTTGCTGTAATCACCCGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt                     <  1:5504730/71‑1 (MQ=255)
                                                 tCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagt                        <  1:221067/67‑1 (MQ=255)
                                                 tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                             <  1:186794/46‑1 (MQ=255)
                                                 tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                                   <  1:4401480/56‑1 (MQ=255)
                                                 tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                                   <  1:5094596/56‑1 (MQ=255)
                                                  cGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCg                   >  1:2755171/1‑71 (MQ=255)
                                                   ggCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTacg                                       >  1:1250668/1‑50 (MQ=255)
                                                   ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                                    >  1:5260328/1‑37 (MQ=255)
                                                   ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg                  >  1:4789844/1‑71 (MQ=255)
                                                    gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACg                               <  1:2905550/57‑1 (MQ=255)
                                                     cacaATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                                  >  1:4143862/1‑37 (MQ=255)
                                                     cacaATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                                  >  1:4058507/1‑37 (MQ=255)
                                                      acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                                   <  1:3420530/51‑1 (MQ=255)
                                                      acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa               <  1:4583160/71‑1 (MQ=255)
                                                       caATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa               <  1:490495/70‑1 (MQ=255)
                                                        aaTATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                                  <  1:3048315/50‑1 (MQ=255)
                                                        aaTATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATa             <  1:5124843/71‑1 (MQ=255)
                                                          tatGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTTCGCTCAAACGATGTGGTGATCGGTAATACg           <  1:3512811/71‑1 (MQ=255)
                                                           atGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag                         <  1:2164032/56‑3 (MQ=255)
                                                           atGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag                         <  1:1144911/56‑3 (MQ=255)
                                                           atGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag                         <  1:2080798/56‑3 (MQ=255)
                                                            tGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCg                   <  1:3453030/61‑1 (MQ=255)
                                                            tGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCg                   <  1:1206339/61‑1 (MQ=255)
                                                             gCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTc                                    <  1:1286203/43‑1 (MQ=12)
                                                             gCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagtc                       >  1:1265162/1‑55 (MQ=255)
                                                                ggTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                          <  1:5346000/50‑1 (MQ=255)
                                                                ggTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtgg                         >  1:1739802/1‑51 (MQ=255)
                                                                  ttGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACGATATCTGc   <  1:686288/71‑1 (MQ=255)
                                                                  ttGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACGATATCTGc   >  1:1784590/1‑71 (MQ=255)
                                                                   tGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACGATATCTGCg  >  1:4543770/1‑71 (MQ=255)
                                                                    |                                                                     
ACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACGATATCTGCG  >  minE/1259293‑1259430

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