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 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,554,520 G→T 22.3% L40I (CTC→ATC)  envC ← protease with a role in cell division

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,554,5200GT22.3% 277.4 / 41.4 107L40I (CTC→ATC) envCprotease with a role in cell division
Reads supporting (aligned to +/- strand):  ref base G (46/37);  new base T (10/14);  total (56/51)
Fisher's exact test for biased strand distribution p-value = 2.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

Only 100 of 111 total aligned reads displayed.

CTTGCGCGTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGCGTA  >  minE/2554450‑2554589
                                                                      |                                                                     
cTTGCGCGTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAg                                                                       <  1:4211305/71‑1 (MQ=255)
 ttGCGCGTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGt                                                                      >  1:4201397/1‑71 (MQ=255)
   gcgcGTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTg                                                                    >  1:4130984/1‑71 (MQ=255)
    cgcgTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTgg                                                                   >  1:896916/1‑71 (MQ=255)
       gttgttgttGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCa                                                                >  1:3794050/1‑71 (MQ=255)
        ttgttgttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAg                                                                       <  1:4678045/63‑1 (MQ=255)
        ttgttgttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTg                                                                    <  1:2066824/66‑1 (MQ=255)
        ttgttgttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCa                                                                <  1:4668672/70‑1 (MQ=255)
           ttgttgCTTTTGGCGTACCGCGCGCTCTTTTGCTGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGc                                                             <  1:1794837/70‑1 (MQ=255)
           ttgttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGc                                                             <  1:4595933/70‑1 (MQ=255)
             gttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAgatttgattt                                                                     >  1:1855138/1‑60 (MQ=255)
             gttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTc                                                           >  1:4425260/1‑70 (MQ=255)
             gttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTc                                                           <  1:1103938/70‑1 (MQ=255)
              ttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTTAATAGATTTGAGTTGGTCACGCTCAt                                                         <  1:2419195/71‑1 (MQ=255)
              ttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCa                                                          <  1:3767724/70‑1 (MQ=255)
              ttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCa                                                          <  1:326063/70‑1 (MQ=255)
              ttgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCa                                                          <  1:4065679/70‑1 (MQ=255)
               tgCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATc                                                        >  1:3451297/1‑71 (MQ=255)
                   tttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCcgcg                                                    >  1:4367635/1‑71 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTTAATAGATTTGAGTTGGTCACGCTCATCCGCGt                                                   >  1:1887018/1‑71 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGt                                                                  >  1:2265990/1‑56 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCcgc                                                     <  1:4165973/69‑1 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCcgcg                                                    <  1:3995570/70‑1 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCcgc                                                     <  1:4254237/69‑1 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGt                                                   >  1:4331507/1‑71 (MQ=255)
                    ttGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGt                                                   >  1:1213677/1‑71 (MQ=255)
                      ggCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTgg                                                 >  1:2230405/1‑71 (MQ=255)
                       gCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTggg                                                >  1:1301500/1‑71 (MQ=255)
                          tACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGtt                                                                     <  1:2490098/47‑1 (MQ=255)
                          tACCGCGCGCTCTTTCGCGGCGATGTCAGCCTGAATGGATTTGAGTTGGTCACGCTCATCCGCGTGGGCg                                              >  1:743041/1‑70 (MQ=255)
                            ccGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaa                                           <  1:1388438/71‑1 (MQ=255)
                            ccGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaa                                           <  1:3392000/71‑1 (MQ=255)
                            ccGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaa                                           <  1:2866088/71‑1 (MQ=255)
                            ccGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGa                                            >  1:1603027/1‑70 (MQ=255)
                            ccGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGa                                            <  1:1079718/70‑1 (MQ=255)
                            ccGCGCGCTCTTTTGAGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGa                                            >  1:1461269/1‑70 (MQ=255)
                              gcgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCAc                                                               >  1:3809318/1‑49 (MQ=255)
                              gcgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaaaa                                         <  1:3892718/71‑1 (MQ=255)
                              gcgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaaaa                                         <  1:4418700/71‑1 (MQ=255)
                               cgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAg                                        <  1:40655/71‑1 (MQ=255)
                               cgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTggg                                                >  1:221495/1‑63 (MQ=255)
                               cgcgcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAg                                        >  1:962510/1‑71 (MQ=255)
                                  gcTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCa                                                          <  1:3564815/50‑1 (MQ=255)
                                   ctctTTTGCGGCGATGTCAGCCTGAATAGATTTGAg                                                                       >  1:147114/1‑36 (MQ=255)
                                     ctTTTGCGGCGATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGca                                   >  1:954815/1‑70 (MQ=255)
                                      ttttGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGcac                                  >  1:1012288/1‑70 (MQ=255)
                                        ttGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGgcg                                     >  1:2418939/1‑65 (MQ=255)
                                        ttGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGgc                                      >  1:1999336/1‑64 (MQ=255)
                                        ttGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGgc                                      >  1:248888/1‑64 (MQ=255)
                                        ttGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaa                                >  1:2038301/1‑70 (MQ=255)
                                         tGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACg                                                              >  1:246218/1‑39 (MQ=255)
                                         tGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACg                                                              >  1:2287367/1‑39 (MQ=255)
                                         tGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               <  1:4024044/70‑1 (MQ=255)
                                           cggcgATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCAcaacaa                             <  1:1851367/70‑1 (MQ=255)
                                            ggcgATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGaaaa                                         <  1:2678541/57‑1 (MQ=255)
                                             gcgATGTCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATAc                          >  1:1027357/1‑71 (MQ=255)
                                               gATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGGGCACAACAATACGc                        >  1:2438586/1‑71 (MQ=255)
                                                  gTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTg                                                  >  1:2474515/1‑42 (MQ=255)
                                                   tCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               >  1:1097254/1‑60 (MQ=255)
                                                   tCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCAcaacaa                             <  1:2341326/62‑1 (MQ=255)
                                                   tCAGCCTGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAg                     <  1:1604373/70‑1 (MQ=255)
                                                   tCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCcgc                                                     <  1:1457150/38‑1 (MQ=255)
                                                   tCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCcgc                                                     <  1:4187756/38‑1 (MQ=255)
                                                   tCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCcg                                                      <  1:555603/37‑1 (MQ=255)
                                                   tCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAgc                    >  1:4499832/1‑71 (MQ=255)
                                                    cAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTTGGCGGAAAAGGCGCACAACAATa                           >  1:2547965/1‑63 (MQ=255)
                                                     aGCCTGAATAGATTTGAGTTGGTCACGCTCATCcgcg                                                    >  1:392401/1‑37 (MQ=255)
                                                     aGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCg                                              >  1:2052607/1‑43 (MQ=255)
                                                     aGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCAcaacaa                             <  1:1639565/60‑1 (MQ=255)
                                                       ccTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCt                 <  1:3971908/70‑1 (MQ=255)
                                                        cTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaaaa                                         >  1:3378014/1‑45 (MQ=255)
                                                        cTGAATAGATTTGAGTAGGTCACGCTCATCCGCGTGGGCGGaaaa                                         >  1:4691571/1‑45 (MQ=255)
                                                         tGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               <  1:2744773/54‑1 (MQ=255)
                                                         tGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               <  1:3270942/54‑1 (MQ=255)
                                                         tGAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               <  1:3386612/54‑1 (MQ=255)
                                                          gAATAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAg                                        >  1:4407099/1‑44 (MQ=255)
                                                          gAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaa                                           <  1:3591107/41‑1 (MQ=255)
                                                           aaTAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCacaac                               >  1:4617936/1‑52 (MQ=255)
                                                           aaTAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAg              <  1:500101/69‑1 (MQ=255)
                                                           aaTAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGaa            >  1:755876/1‑71 (MQ=255)
                                                            aTAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAAc           >  1:3934990/1‑71 (MQ=255)
                                                             tAGATTTGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACg          >  1:3569739/1‑71 (MQ=255)
                                                             tAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaaa                                          <  1:1998371/39‑1 (MQ=255)
                                                             tAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAg              <  1:1770063/67‑1 (MQ=255)
                                                              aGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATa                           >  1:720627/1‑53 (MQ=255)
                                                               gATTTGAGTTGGTGACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCt        >  1:3660083/1‑71 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGc         <  1:1663812/70‑1 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGc         <  1:1192440/70‑1 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGc         <  1:940663/70‑1 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCt        >  1:2838258/1‑71 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCt        >  1:2449991/1‑71 (MQ=255)
                                                               gATTTGAGTTGGTCACGCTAATCCGCGTGGGCGGAAAAGGCGCACAACAATa                           >  1:3616884/1‑52 (MQ=255)
                                                                aTTTGAGTTGGTCACGCTCATCCGCGTGGGCGGaa                                           <  1:2518606/35‑1 (MQ=255)
                                                                 tttGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTgg      <  1:2572927/71‑1 (MQ=255)
                                                                  ttGATTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGc     >  1:2101132/1‑71 (MQ=255)
                                                                  ttGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGc     >  1:1545950/1‑71 (MQ=255)
                                                                  ttGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGc     >  1:4170224/1‑71 (MQ=255)
                                                                  ttGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGc     >  1:3990223/1‑71 (MQ=255)
                                                                   tGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGCg    >  1:1590347/1‑71 (MQ=255)
                                                                     aGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGCGTa  <  1:1150820/71‑1 (MQ=255)
                                                                      |                                                                     
CTTGCGCGTTGTTGTTGCTTTTGGCGTACCGCGCGCTCTTTTGCGGCGATGTCAGCCTGAATAGATTTGAGTTGGTCACGCTCATCCGCGTGGGCGGAAAAGGCGCACAACAATACGCCAGCGCTAAGAACGCTGGCGTA  >  minE/2554450‑2554589

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