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 1,181,303 A→G 46.6% H109R (CAT→CGT)  yeaD → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,181,3030AG46.6% 10.0 / 103.8 118H109R (CAT→CGT) yeaDconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (17/46);  new base G (24/31);  total (41/77)
Fisher's exact test for biased strand distribution p-value = 8.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 127 total aligned reads displayed.

GCACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTG  >  minE/1181239‑1181369
                                                                |                                                                  
gcACAACAAGGTCTGTCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2087642/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2846767/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2281869/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1637794/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1684771/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:279949/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2114716/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:740157/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1822952/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2942208/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:3051288/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1218878/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:182378/69‑1 (MQ=255)
gcACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1925952/69‑1 (MQ=255)
 cacaACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:664689/68‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2135703/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2619425/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:556401/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:884227/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:2424362/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:1133102/67‑1 (MQ=255)
  acaacaAGGTCTGCCTGCGCAAGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGaa                                                                <  1:3125959/67‑1 (MQ=255)
      caaGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCt                                                          <  1:2236770/69‑1 (MQ=255)
      caaGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCt                                                          <  1:2216666/69‑1 (MQ=255)
      caaGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCt                                                          <  1:450040/69‑1 (MQ=255)
       aaGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCt                                                          <  1:1646883/68‑1 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2466599/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2578607/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2583236/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2660370/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2855625/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:2904210/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:3068013/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:3134021/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1144057/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1454360/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:739244/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1397116/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1235439/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:521125/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1373847/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1584918/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1600194/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATgg                                                     >  1:1634580/1‑68 (MQ=255)
            ctgcctgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATgg                                                     >  1:933176/1‑68 (MQ=255)
                 tgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGt                                                  <  1:1207970/66‑1 (MQ=255)
                 tgcGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGt                                                  <  1:2506314/66‑1 (MQ=255)
                 tgcGCACGGTTTTGCCAGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGt                                                  <  1:2192079/66‑1 (MQ=255)
                  gcgcACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGt                                                  <  1:1462788/65‑1 (MQ=255)
                   cgcACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAgcg                                              >  1:1297594/1‑68 (MQ=255)
                   cgcACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAgcg                                              >  1:265744/1‑68 (MQ=255)
                   cgcACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAgcg                                              >  1:3327626/1‑68 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:1364393/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2892967/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2915817/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:784907/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2789442/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:3311761/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:470919/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:672810/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:1926510/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:43336/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:3422060/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2067189/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:176861/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:1746384/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2210659/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2410989/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:611744/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:1563768/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:2464293/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:3329262/68‑1 (MQ=255)
                              gCCCGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:682508/68‑1 (MQ=255)
                               cccGCAACCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACTTTTGa                                   <  1:3341039/67‑1 (MQ=255)
                                     aCCTGCCGTGGACGCTGAAATCACATCGTGAAGATGCTGATGGTGTAGTGCTAACttttta                                   <  1:3050517/61‑3 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:2422939/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:1324774/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:1439140/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:1736295/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:2049449/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:1830821/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCg                     <  1:1889318/68‑1 (MQ=255)
                                            gTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCCCTGACTTTTGAATTGACGCAAAGCg                     <  1:1932878/68‑1 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAgcgc                                             >  1:2690260/1‑41 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAaga                 >  1:1229566/1‑69 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAaga                 >  1:725564/1‑69 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAaga                 >  1:2485905/1‑69 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAaga                 >  1:2624875/1‑69 (MQ=255)
                                               gACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAaga                 >  1:3097767/1‑69 (MQ=255)
                                                 cGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAagag                >  1:1458013/1‑68 (MQ=255)
                                                     gAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGATTTGACGCAAAGCg                     <  1:1567840/59‑1 (MQ=255)
                                                           acaTCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAAtt     >  1:535590/1‑69 (MQ=255)
                                                           acaTCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAAtt     >  1:2114147/1‑69 (MQ=255)
                                                           acaTCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAAtt     >  1:1163246/1‑69 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCt   >  1:1409100/1‑68 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTg  >  1:1144976/1‑69 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTg  >  1:938726/1‑69 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTg  >  1:1514607/1‑69 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTg  >  1:19325/1‑69 (MQ=255)
                                                              tcatGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTg  >  1:322021/1‑69 (MQ=255)
                                                                |                                                                  
GCACAACAAGGTCTGCCTGCGCACGGTTTTGCCCGCAACCTGCCGTGGACGCTGAAATCACATCATGAAGATGCTGATGGCGTAGCGCTGACTTTTGAATTGACGCAAAGCGAAGAGACGAAAAAATTCTG  >  minE/1181239‑1181369

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