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 1,259,351 T→G 17.7% 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
*minE1,259,3510TG17.7% 184.1 / 49.5 102I525L (ATT→CTT) ‡torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base T (43/41);  new base G (14/4);  total (57/45)
Fisher's exact test for biased strand distribution p-value = 6.51e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 103 total aligned reads displayed.

TCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATAC  >  minE/1259284‑1259420
                                                                   |                                                                     
tCGGCAAACACGGCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                    <  1:1939879/71‑1 (MQ=255)
   gCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTg                                                                 <  1:1539223/71‑1 (MQ=255)
   gCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTg                                                                 >  1:576774/1‑71 (MQ=255)
       acacGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTg                                                             <  1:2929217/71‑1 (MQ=255)
        cacGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGc                                                            <  1:544249/71‑1 (MQ=255)
           gTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                           >  1:2098813/1‑69 (MQ=255)
           gTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTg                                                          >  1:3067295/1‑70 (MQ=255)
           gTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGt                                                         <  1:504385/71‑1 (MQ=255)
           atCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGt                                                         <  1:1807957/70‑1 (MQ=255)
            tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                        <  1:188086/71‑1 (MQ=255)
             cAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGc                                                                   >  1:44713/1‑59 (MQ=255)
             cAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTaa                                                       >  1:165247/1‑71 (MQ=255)
              aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                      <  1:2587043/71‑1 (MQ=255)
              aaaaTCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTAAt                                                      <  1:337808/71‑1 (MQ=255)
               aaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                    >  1:2273071/1‑56 (MQ=255)
               aaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGc                                                                   >  1:1347719/1‑57 (MQ=255)
               aaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                      >  1:1249524/1‑70 (MQ=255)
                 aTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                   <  1:470536/71‑1 (MQ=255)
                 aTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                   <  1:1778016/71‑1 (MQ=255)
                  tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAcc                                                  >  1:3372617/1‑71 (MQ=255)
                  tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAcc                                                  >  1:513725/1‑71 (MQ=255)
                  tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAcc                                                  >  1:3105599/1‑71 (MQ=255)
                   cGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCg                                                 >  1:3200162/1‑71 (MQ=255)
                   cGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCg                                                 >  1:3768493/1‑71 (MQ=255)
                   cGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCg                                                 >  1:151080/1‑71 (MQ=255)
                    gTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCgg                                                >  1:455261/1‑71 (MQ=255)
                    gTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCg                                                 >  1:128098/1‑70 (MQ=255)
                    gTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCg                                                 >  1:746990/1‑70 (MQ=255)
                     ttACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                    <  1:2040405/50‑1 (MQ=255)
                       aCGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTc                                              <  1:2202681/70‑1 (MQ=255)
                        cgcgCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCAt                                            <  1:1215971/71‑1 (MQ=255)
                         gcgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           >  1:3400514/1‑71 (MQ=255)
                           gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGt                                         >  1:1666713/1‑71 (MQ=255)
                           gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGt                                         >  1:3452958/1‑71 (MQ=255)
                            cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATc                                                     <  1:397559/58‑1 (MQ=255)
                              tCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGc                                                            >  1:1738389/1‑49 (MQ=255)
                                aaaTTGCTGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAg                                     <  1:921377/70‑1 (MQ=255)
                                 aaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAg                                     >  1:1433139/1‑69 (MQ=255)
                                  aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                  <  1:1517939/71‑1 (MQ=255)
                                      cGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTgc                              >  1:3544148/1‑71 (MQ=255)
                                         aGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCt                           >  1:2405667/1‑71 (MQ=255)
                                         aGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCt                           >  1:3029568/1‑71 (MQ=255)
                                          gCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                 >  1:3250342/1‑64 (MQ=255)
                                            aaCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                             <  1:2219828/50‑1 (MQ=255)
                                            aaCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                  <  1:2682738/61‑1 (MQ=255)
                                             aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                 <  1:1403782/61‑1 (MQ=255)
                                              cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                      >  1:231363/1‑71 (MQ=255)
                                              cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATAACCGGTCATAGTCAAGTCATTGCGCTCaaa                       >  1:531696/1‑70 (MQ=255)
                                              cAGCCTGCTTCATCGGCACAATATCCTGGTTGCTGTAATCAc                                                   >  1:791073/1‑42 (MQ=255)
                                                gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGATCAAACGa                    <  1:828043/71‑1 (MQ=255)
                                                  cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                  <  1:2783061/71‑1 (MQ=255)
                                                  cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                  <  1:3004255/71‑1 (MQ=255)
                                                  cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                  <  1:3891486/71‑1 (MQ=255)
                                                   tGCTTCATCGGCACCAGATGCTGATTACTGTAATCa                                                    >  1:3555863/1‑36 (MQ=19)
                                                   tGCTTCATCGGCACCAGATGCTGATTACTGTAATCa                                                    >  1:454530/1‑36 (MQ=19)
                                                   tGCTTCATCGGCACCAGATGCTGATTACTGTAATCa                                                    >  1:2650871/1‑36 (MQ=19)
                                                   tGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                  >  1:3640263/1‑68 (MQ=255)
                                                   tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGTTCATCGTCAAGTCATTGCGCTCAAACGAtgt                 >  1:3010057/1‑71 (MQ=255)
                                                   tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGt                                               <  1:1314366/41‑1 (MQ=255)
                                                   tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           <  1:412213/45‑1 (MQ=255)
                                                   tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           <  1:1062837/45‑1 (MQ=255)
                                                   tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           <  1:2943726/45‑1 (MQ=255)
                                                    gCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCAtgg                                          >  1:3190134/1‑43 (MQ=255)
                                                    gCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                  >  1:2397924/1‑67 (MQ=255)
                                                    gCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                  >  1:1256085/1‑67 (MQ=255)
                                                    gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                >  1:3578712/1‑71 (MQ=255)
                                                     cTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag               <  1:2453958/71‑3 (MQ=255)
                                                     cTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag               >  1:2750524/1‑69 (MQ=255)
                                                     cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTgc                              <  1:1701252/56‑1 (MQ=255)
                                                     cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg                <  1:1514050/70‑1 (MQ=255)
                                                      ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagt              >  1:1730518/1‑71 (MQ=255)
                                                      ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           >  1:771381/1‑42 (MQ=255)
                                                      ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                           >  1:282319/1‑42 (MQ=255)
                                                       tCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCaaa                       >  1:1632711/1‑61 (MQ=255)
                                                        cATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                        <  1:1577647/59‑1 (MQ=255)
                                                        cATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                        <  1:3494622/59‑1 (MQ=255)
                                                        cATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggtg             <  1:3951101/70‑1 (MQ=255)
                                                         aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                 >  1:2068752/1‑49 (MQ=255)
                                                         aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt           <  1:3708710/71‑1 (MQ=255)
                                                         aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt           >  1:2901012/1‑71 (MQ=255)
                                                         aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt           >  1:1764250/1‑71 (MQ=255)
                                                         aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt           >  1:3490521/1‑71 (MQ=255)
                                                          tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                  <  1:3646008/63‑1 (MQ=255)
                                                          tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggtg             <  1:851301/68‑1 (MQ=255)
                                                           cGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTAAAACGATGTGGTGATCg         >  1:1511245/1‑71 (MQ=255)
                                                            ggCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag               >  1:1710461/1‑62 (MQ=255)
                                                            ggCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAggtag               >  1:888718/1‑62 (MQ=255)
                                                            ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg        >  1:1728536/1‑71 (MQ=255)
                                                             gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                         <  1:1309532/53‑1 (MQ=255)
                                                             gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                         <  1:1157681/53‑1 (MQ=255)
                                                             gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGt       <  1:2305141/71‑1 (MQ=255)
                                                             gCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGt       <  1:440249/71‑1 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                       >  1:1563468/1‑53 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                       >  1:1359624/1‑53 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa     <  1:3484133/71‑1 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa     >  1:2131078/1‑71 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTa      >  1:2015190/1‑70 (MQ=255)
                                                               acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCCCTCAAACGATGTGGTGATCGGTaa     <  1:3065910/71‑1 (MQ=255)
                                                                caATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa     >  1:879018/1‑70 (MQ=255)
                                                                  atatGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATAc  >  1:1187059/1‑71 (MQ=255)
                                                                   |                                                                     
TCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATAC  >  minE/1259284‑1259420

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