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 2,000,410 G→A 36.3% F291F (TTC→TTT)  gss ← fused glutathionylspermidine amidase and glutathionylspermidine synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,000,4100GA36.3% 98.9 / 87.5 143F291F (TTC→TTT) gssfused glutathionylspermidine amidase and glutathionylspermidine synthetase
Reads supporting (aligned to +/- strand):  ref base G (54/37);  new base A (23/29);  total (77/66)
Fisher's exact test for biased strand distribution p-value = 8.54e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.19e-01

Only 100 of 143 total aligned reads displayed.

ATCATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGC  >  minE/2000345‑2000476
                                                                 |                                                                  
aTCATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGaa                                                                  >  1:1211389/1‑68 (MQ=255)
aTCATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAAc                                                                 >  1:2304579/1‑69 (MQ=255)
aTCATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAAc                                                                 >  1:3114384/1‑69 (MQ=255)
aTCATATGGTGACAGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAAc                                                                 >  1:1318246/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:3265999/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:216071/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:2245340/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:1012029/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:2957400/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:1577229/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:3377322/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:620158/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:1233847/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:1147329/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:1176139/1‑69 (MQ=255)
aTCATATGATGACGGCGACGCTGCAAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:117827/1‑69 (MQ=255)
aTCATAGGATGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAAc                                                                 >  1:440321/1‑69 (MQ=255)
  cATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAg                                                               >  1:1673389/1‑69 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGTACAgc                                                              >  1:1488130/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:2563764/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:178561/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:1221748/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:1697797/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:2028223/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:1546710/1‑67 (MQ=255)
     atGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAgc                                                              >  1:2200845/1‑67 (MQ=255)
      tGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCTGAGGATTTTCGGGATGTCGAACAGCGcc                                                           >  1:2908686/1‑69 (MQ=255)
      tGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGcc                                                           >  1:2350718/1‑69 (MQ=255)
      tGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGcc                                                           >  1:1113745/1‑69 (MQ=255)
      tGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGcc                                                           >  1:3230435/1‑69 (MQ=255)
        gTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGcc                                                           >  1:713278/1‑67 (MQ=255)
          gACGGCGACGCTGCCAGGAGAGACGCAAACGTGG‑CAGAGGATTTTCGGGATGTCGAACAGCGCcagcag                                                      <  1:2433765/69‑1 (MQ=255)
           actgCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:1683854/66‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCcagcag                                                      <  1:914342/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCcagcag                                                      <  1:1223797/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:3167279/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:2411637/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:911863/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:1719247/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:127603/69‑1 (MQ=255)
           aCGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:2024159/69‑1 (MQ=255)
            cGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:2759977/68‑1 (MQ=255)
            cGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:3178709/68‑1 (MQ=255)
            cGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:1573374/68‑1 (MQ=255)
                  cGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCcagcag                                                      <  1:616133/62‑1 (MQ=255)
                    cTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATc                                             <  1:606086/69‑1 (MQ=255)
                    cTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATc                                             <  1:737645/69‑1 (MQ=255)
                    cTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATc                                             <  1:73181/69‑1 (MQ=255)
                    cTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATc                                             <  1:1618167/69‑1 (MQ=255)
                     tGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCt                                            <  1:3000952/69‑1 (MQ=255)
                     tGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCt                                            <  1:741178/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:3024725/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:402766/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:1718118/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:2930415/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:368401/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:931025/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:2448416/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:2043057/69‑1 (MQ=255)
                                 cGCAAACGTGGCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:2713314/69‑1 (MQ=255)
                                          ggCCAGAGGATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTg                                <  1:648232/60‑1 (MQ=255)
                                              agagGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGaa                   <  1:711995/69‑1 (MQ=255)
                                              agagGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGaa                   <  1:1760753/69‑1 (MQ=255)
                                              agagGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGaa                   <  1:377723/69‑1 (MQ=255)
                                              agagGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGaa                   <  1:2073934/69‑1 (MQ=255)
                                              agagGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGaa                   <  1:517653/69‑1 (MQ=255)
                                                agGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGa                 <  1:1884461/69‑1 (MQ=255)
                                                 ggATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGa                 >  1:2149814/1‑68 (MQ=255)
                                                 ggATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTGGCGTGAAGa                 >  1:2159196/1‑68 (MQ=255)
                                                 ggATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTGGCGTGAAGa                 >  1:813206/1‑68 (MQ=255)
                                                 ggATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTGGCGTGAAGa                 >  1:1675583/1‑68 (MQ=255)
                                                 ggATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTGGCGTGAAGa                 >  1:2047401/1‑68 (MQ=255)
                                                 ggATTTTCGGAATGTCAAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTGGCGTGAAGa                 >  1:1786702/1‑68 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:456162/69‑1 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:69413/69‑1 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:2071786/69‑1 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:1884516/69‑1 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:2788911/69‑1 (MQ=255)
                                                   aTTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:3219157/69‑1 (MQ=255)
                                                    ttttCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATAc              <  1:3106407/68‑1 (MQ=255)
                                                        cGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCa          <  1:963303/68‑1 (MQ=255)
                                                        cGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCa          <  1:1963391/68‑1 (MQ=255)
                                                        cGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCa          <  1:468608/68‑1 (MQ=255)
                                                        cGGGATGTCGAACAGCGCCAGCAGGTTGGCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCa          <  1:1187539/68‑1 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAgg        >  1:3314308/1‑63 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGc     >  1:2986861/1‑66 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:1343231/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2910978/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:675673/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:1412233/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2656574/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2450666/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:42619/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:1639902/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2241151/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2120032/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:825787/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:1238282/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:2065547/1‑69 (MQ=255)
                                                               tCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGc  >  1:1702877/1‑69 (MQ=255)
                                                                 |                                                                  
ATCATATGGTGACGGCGACGCTGCCAGGAGAGACGCAAACGTGGCCAGAGGATTTTCGGGATGTCGAACAGCGCCAGCAGGTTGTCATCTTTCAGCACCTTGTCGGTTGCGTGAAGATACATCAGGTGCAGC  >  minE/2000345‑2000476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A