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 1,508,705 G→A 36.1% R138R (CGC→CGT)  yfbV ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,508,7050GA36.1% 70.2 / 63.1 105R138R (CGC→CGT) yfbVconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (48/19);  new base A (17/21);  total (65/40)
Fisher's exact test for biased strand distribution p-value = 1.15e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.89e-01

Only 100 of 112 total aligned reads displayed.

TGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACGGGTGCCAACACCTGTCCAG  >  minE/1508645‑1508772
                                                            |                                                                   
tGCGTAATCAGGGGTCAATTACAAATCATCAAGTAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:2298807/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:2350448/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:2055149/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:782189/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:1977384/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:3305905/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:381996/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:388203/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:1512906/68‑1 (MQ=255)
tGCGTAATCAGGGGTCAATTACAAATAATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:3252171/68‑1 (MQ=255)
tGCGTAATCAGGGGGCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:2508854/68‑1 (MQ=255)
    tAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:1035828/69‑1 (MQ=255)
    tAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:224341/69‑1 (MQ=255)
    tAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:2040799/69‑1 (MQ=255)
    tAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:1744217/69‑1 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtgt                                                        >  1:3258258/1‑68 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:452470/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:1712889/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:2281860/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:536764/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:1798632/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:3356381/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:585920/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:1833124/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:1319526/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:2932853/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:777908/1‑69 (MQ=255)
      aTCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:2005237/1‑69 (MQ=255)
         aGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAg                                                     >  1:644362/1‑68 (MQ=255)
         aGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAg                                                     >  1:3252125/1‑68 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:119466/68‑1 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:3244401/68‑1 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:3141817/68‑1 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:1130234/68‑1 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:851963/68‑1 (MQ=255)
           gggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:526203/68‑1 (MQ=255)
            ggTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   <  1:1189650/67‑1 (MQ=255)
             gTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCACGCTTaa                                                              <  1:2017022/55‑1 (MQ=255)
                aaTTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGcc                                             >  1:451006/1‑69 (MQ=255)
                aaTTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGcc                                             >  1:971368/1‑69 (MQ=255)
                aaTTAAAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGATaa                                                 >  1:1227938/1‑65 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:2266805/54‑1 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:869620/54‑1 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:806426/54‑1 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:1211071/54‑1 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgtg                                                         <  1:2673120/54‑1 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:3272309/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:477251/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:39622/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:3039723/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:2334822/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:2350527/1‑53 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   >  1:2607860/1‑60 (MQ=255)
                   tACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCt                                                   >  1:1285287/1‑60 (MQ=255)
                   tACAAATCATAAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCgt                                                          >  1:1813861/1‑53 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGTGTGTCAGCTAATGCCTGGt                                         >  1:2507082/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:1851314/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:3290408/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:1818814/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:2095073/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:1401100/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGt                                         >  1:2190037/1‑69 (MQ=255)
                    aCAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGACTGGt                                         >  1:2490347/1‑69 (MQ=255)
                         tcatcaAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTGATGCCTGGTAATCa                                    <  1:1422306/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:527524/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:474501/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:540897/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:2241934/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:1018938/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:2174067/69‑1 (MQ=255)
                                  aaaGTTTTATCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           <  1:2723558/69‑1 (MQ=255)
                                   aaGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           >  1:2322105/1‑68 (MQ=255)
                                   aaGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           >  1:2869118/1‑68 (MQ=255)
                                   aaGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCt                           >  1:885288/1‑68 (MQ=255)
                                        ttATCCAGTTGTTTGAATGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACg                     >  1:665026/1‑69 (MQ=255)
                                        ttATCCAGTTGTTTGAAGGCGTGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACg                     >  1:654676/1‑69 (MQ=255)
                                        ttATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTc                                                       >  1:84620/1‑35 (MQ=255)
                                        ttATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACg                     >  1:2733521/1‑69 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAg                                   >  1:3408140/1‑53 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGc                                 >  1:3136486/1‑55 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:222734/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2625075/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2720958/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:1119764/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:1352046/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:1827667/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2797252/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2340906/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:1472047/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2193021/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:1514843/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:363990/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:3322585/1‑56 (MQ=255)
                                          aTCCAGTTGTTTGAAGGCACGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCt                                >  1:2257875/1‑56 (MQ=255)
                                                           cgcgcTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACGGGTGCCAACACCTGTCCAg  <  1:1458760/69‑1 (MQ=255)
                                                            gcgcTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTc                         <  1:3067801/45‑1 (MQ=255)
                                                            gcgcTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTc                         <  1:1787098/45‑1 (MQ=255)
                                                            gcgcTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTc                         <  1:2092490/45‑1 (MQ=255)
                                                            gcgcTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTc                         <  1:1909123/45‑1 (MQ=255)
                                                            gcgcTTAAGCGTGTCAGCTAATGCCTGCTAATCAGGCTTGCCTTc                         <  1:2358240/45‑1 (MQ=255)
                                                            |                                                                   
TGCGTAATCAGGGGTCAATTACAAATCATCAAGGAAAGTTTTATCCAGTTGTTTGAAGGCGCGCTTAAGCGTGTCAGCTAATGCCTGGTAATCAGGCTTGCCTTCAACGGGTGCCAACACCTGTCCAG  >  minE/1508645‑1508772

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