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 1,449,165 A→G 44.2% Q524R (CAA→CGA)  atoS → sensory histidine kinase in two‑component regulatory system with AtoC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,449,1650AG44.2% 24.4 / 93.3 113Q524R (CAA→CGA) atoSsensory histidine kinase in two‑component regulatory system with AtoC
Reads supporting (aligned to +/- strand):  ref base A (30/33);  new base G (13/37);  total (43/70)
Fisher's exact test for biased strand distribution p-value = 2.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.08e-02

Only 100 of 130 total aligned reads displayed.

CTACTGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTGGCATTG  >  minE/1449104‑1449227
                                                             |                                                              
ctactGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTg                                                          >  1:1153204/1‑68 (MQ=255)
  actTAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:2904150/1‑60 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:2173607/1‑60 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                <  1:505401/60‑1 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:2408954/1‑60 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:2858956/1‑60 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                <  1:1946323/60‑1 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                <  1:1610935/60‑1 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                <  1:1712866/60‑1 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:257513/1‑60 (MQ=255)
  actGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:2551468/1‑60 (MQ=255)
  actGAATATCCTGATCAATGACGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCa                                                                >  1:101861/1‑60 (MQ=255)
     gAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:761387/67‑1 (MQ=255)
     gAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:1495167/67‑1 (MQ=255)
     gAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:1663734/67‑1 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:595410/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:1936701/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:195473/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:2236183/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:2083292/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:2469579/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:59150/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:510310/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:2796989/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTata                                                  >  1:12699/1‑66 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2372602/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:235193/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2342260/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2844645/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2941292/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2978200/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:3285189/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:3265581/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:102179/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1983580/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1963489/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:2071841/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1071942/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:848917/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1448491/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1012612/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1194441/67‑2 (MQ=255)
        tatCCTGATCAATGCCGTCCAGGCTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGCCAGTat                                                   <  1:3077125/67‑2 (MQ=255)
         atCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGc                                                <  1:1281718/69‑1 (MQ=255)
          tCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGc                                                >  1:55848/1‑68 (MQ=255)
          tCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCg                                               >  1:1240268/1‑69 (MQ=255)
          tCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCg                                               >  1:84124/1‑69 (MQ=255)
          tCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCg                                               >  1:2378509/1‑69 (MQ=255)
          tCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCg                                               >  1:658808/1‑69 (MQ=255)
            cTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGAc                                             <  1:2676514/69‑1 (MQ=255)
            cTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGAc                                             <  1:184743/69‑1 (MQ=255)
              gATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACt                                            <  1:2590189/68‑1 (MQ=255)
                 cAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTcac                                         >  1:943828/1‑68 (MQ=255)
                    tGCCGTCCAGGCTATCAGTGCACGAGTGAAAATTCGTATTCGAACCTGGCAGTat                                                   <  1:1761224/55‑2 (MQ=25)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:2886098/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:2488233/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:1134164/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:1496253/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:2403168/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:3103783/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCaa                                                      <  1:738711/50‑1 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAg                                    >  1:2420907/1‑68 (MQ=255)
                      ccGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAg                                    >  1:2135882/1‑68 (MQ=255)
                               cTATCAGTGCACTAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:263251/69‑1 (MQ=25)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2618777/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:1232717/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2793104/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2784673/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2760562/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2646710/69‑1 (MQ=37)
                               cTATCAGTGCACGAGGGAAAATTCGTATTCGAACCTGGCAGTATAGCGACTCGCAACAGGCCATTTCGa                          <  1:2143471/69‑1 (MQ=37)
                               cTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:3004473/1‑67 (MQ=255)
                                        cACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACa                 <  1:650196/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:819696/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:759604/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:958232/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:321168/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:3197472/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:1425343/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:1553342/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:1744162/69‑1 (MQ=255)
                                                  aaTTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTgg       <  1:226194/69‑1 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:1232005/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:945743/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:1312101/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:1326208/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:1457520/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:768781/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:1766940/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:2239099/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:2399684/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:2541212/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:2679927/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:3124956/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:345217/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:3202375/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTc                            >  1:3254354/1‑38 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTTGCATTg  <  1:6435/64‑1 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTGGCATTg  <  1:2630139/64‑1 (MQ=255)
                                                            cAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGACTGTGGCATTg  <  1:3420856/64‑1 (MQ=255)
                                                             |                                                              
CTACTGAATATCCTGATCAATGCCGTCCAGGCTATCAGCGCACGAGGGAAAATTCGCATTCAAACCTGGCAATACAGCGACTCACAACAGGCCATTTCGATAGAGGACAACGGCTGTGGCATTG  >  minE/1449104‑1449227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A