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 1,259,351 T→G 22.6% I525L (ATT→CTT) ‡ 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
*minE1,259,3510TG22.6% 250.7 / 106.4 164I525L (ATT→CTT) ‡torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base T (66/61);  new base G (17/20);  total (83/81)
Fisher's exact test for biased strand distribution p-value = 5.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.90e-01

Only 100 of 171 total aligned reads displayed.

GATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACG  >  minE/1259282‑1259421
                                                                     |                                                                      
gATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAata                                                                       >  1:2673821/1‑71 (MQ=255)
  tCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAatat                                                                      >  1:4082233/1‑70 (MQ=255)
     gCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTg                                                                  <  1:4203601/71‑1 (MQ=255)
       aaaaACATCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTgat                                                                <  1:2588035/71‑3 (MQ=255)
           acatCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCt                                                                   <  1:2192890/61‑1 (MQ=255)
            catCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTg                                                           >  1:316453/3‑71 (MQ=255)
              tCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTa                                                         <  1:1852202/71‑1 (MQ=255)
              tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                         <  1:1980557/71‑1 (MQ=255)
              tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                         <  1:832803/71‑1 (MQ=255)
               cAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTaa                                                        >  1:446779/1‑71 (MQ=255)
                aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTaa                                                        >  1:1025002/1‑70 (MQ=255)
                aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                       >  1:283912/1‑71 (MQ=255)
                aaaaTCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGAtta                                                              >  1:3493256/1‑63 (MQ=255)
                    tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                            <  1:5148167/62‑1 (MQ=255)
                    tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAcc                                                   >  1:1424967/1‑71 (MQ=255)
                      gTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCgg                                                 >  1:1723786/1‑71 (MQ=255)
                         aCGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                              >  1:836881/1‑71 (MQ=255)
                          cgcgCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                              <  1:498131/70‑1 (MQ=255)
                           gcgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                            <  1:1981736/71‑1 (MQ=255)
                           gcgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                            <  1:5524540/71‑1 (MQ=255)
                            cgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                     >  1:1939929/1‑45 (MQ=255)
                            cgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                     >  1:5430121/1‑45 (MQ=255)
                             gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                    >  1:5050578/1‑61 (MQ=255)
                             gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGt                                          >  1:189498/1‑71 (MQ=255)
                             gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGt                                          >  1:54923/1‑71 (MQ=255)
                              cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                            >  1:5582834/1‑52 (MQ=255)
                               ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGt                                                          <  1:937645/53‑1 (MQ=255)
                                tCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                         >  1:856251/1‑69 (MQ=255)
                                 cAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCa                                        <  1:3461462/69‑1 (MQ=255)
                                  aaaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                            >  1:1534788/1‑64 (MQ=255)
                                    aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCt                                                                   <  1:4155405/39‑1 (MQ=255)
                                    aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCt                                                                   <  1:3466968/39‑1 (MQ=255)
                                    aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                            <  1:4320656/46‑1 (MQ=255)
                                     ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAtac                                                     >  1:1033626/1‑50 (MQ=255)
                                     ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                  >  1:4026285/1‑71 (MQ=255)
                                     ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                  <  1:5566292/71‑1 (MQ=255)
                                       gCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                 <  1:5179392/70‑1 (MQ=255)
                                        cGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGt                                                                <  1:2151936/38‑1 (MQ=255)
                                             cAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTc                           >  1:3774467/1‑70 (MQ=255)
                                               aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCTTCAAGTCATTGCGCTCaaa                        >  1:5316869/1‑71 (MQ=255)
                                               aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                 >  1:5518979/1‑62 (MQ=255)
                                               aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                                 >  1:4889175/1‑62 (MQ=255)
                                               aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                        >  1:4710690/1‑71 (MQ=255)
                                               aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                        >  1:3573577/1‑71 (MQ=255)
                                               aCAGCCTGCTTCATAGGCACAATATGCTGGTTGATGt                                                          >  1:5093352/1‑37 (MQ=38)
                                                cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                     <  1:878753/57‑1 (MQ=255)
                                                cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       >  1:5322952/1‑71 (MQ=255)
                                                cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       <  1:658400/71‑1 (MQ=255)
                                                cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       <  1:1167206/71‑1 (MQ=255)
                                                 aGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       >  1:1588531/1‑70 (MQ=255)
                                                 aGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       >  1:4465805/1‑70 (MQ=255)
                                                  gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                   >  1:3182833/1‑57 (MQ=255)
                                                  gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                   >  1:909550/1‑57 (MQ=255)
                                                  gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGa                     >  1:2465211/1‑71 (MQ=255)
                                                   cttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGag                    >  1:1603803/3‑70 (MQ=255)
                                                   ccTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                         <  1:320250/66‑1 (MQ=255)
                                                   ccTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                         <  1:2712168/66‑1 (MQ=255)
                                                    ttGCTTCATCGGCACCAGATGCTGATTACTGTAAt                                                       >  1:3487193/2‑35 (MQ=19)
                                                    ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCAcc                                                   <  1:418941/38‑1 (MQ=25)
                                                    ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                 <  1:2268699/56‑1 (MQ=255)
                                                    ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                 <  1:1105413/56‑1 (MQ=255)
                                                    ttGCTTCATCGGCACCAGATGCTGAATACTGTAATCACCGGTCATGGTGAGATCATTACGCTCaaaag                      <  1:3971516/67‑3 (MQ=255)
                                                    cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                   <  1:2590335/71‑1 (MQ=255)
                                                     tGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                   >  1:299908/1‑68 (MQ=255)
                                                     tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCCCTCAAACGAtgt                  >  1:3636816/1‑71 (MQ=255)
                                                      gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                 >  1:3430096/1‑71 (MQ=255)
                                                      gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                 >  1:5045382/1‑71 (MQ=255)
                                                        ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                 >  1:3875618/1‑53 (MQ=255)
                                                        ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                                 >  1:3026116/1‑53 (MQ=255)
                                                        ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                              >  1:2916854/1‑40 (MQ=255)
                                                        ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       <  1:4697260/63‑1 (MQ=255)
                                                        ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                       <  1:5655367/63‑1 (MQ=255)
                                                         tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt               >  1:4743670/1‑70 (MQ=255)
                                                         tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt               >  1:3802995/1‑70 (MQ=255)
                                                          cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                                >  1:4800512/1‑51 (MQ=255)
                                                          cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                                >  1:1386202/1‑51 (MQ=255)
                                                          cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagtc              <  1:1185271/70‑2 (MQ=255)
                                                           aTCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagtcg             >  1:3031055/1‑68 (MQ=255)
                                                           aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt            <  1:820891/71‑1 (MQ=255)
                                                           aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt            <  1:1655858/71‑1 (MQ=255)
                                                            tCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagt               <  1:221067/67‑1 (MQ=255)
                                                            tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                    <  1:186794/46‑1 (MQ=255)
                                                            tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                          <  1:5094596/56‑1 (MQ=255)
                                                            tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                          <  1:4401480/56‑1 (MQ=255)
                                                            tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgt                  <  1:2926890/64‑1 (MQ=255)
                                                             cGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCg          >  1:2755171/1‑71 (MQ=255)
                                                              ggCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTacg                              >  1:1250668/1‑50 (MQ=255)
                                                              ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                           >  1:5523363/1‑37 (MQ=255)
                                                              ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                           >  1:5260328/1‑37 (MQ=255)
                                                              ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg         >  1:3561097/1‑71 (MQ=255)
                                                              ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg         >  1:523185/1‑71 (MQ=255)
                                                              ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg         >  1:4789844/1‑71 (MQ=255)
                                                               gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACg                      <  1:2905550/57‑1 (MQ=255)
                                                                cacaATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                         >  1:4143862/1‑37 (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)
                                                                    atatGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATAc   <  1:3534282/71‑1 (MQ=255)
                                                                     |                                                                      
GATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATACG  >  minE/1259282‑1259421

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