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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,933,155 G→A 30.9% L430L (CTG→TTG) ‡ lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,1550GA30.9% 196.6 / 113.3 149L430L (CTG→TTG) ‡lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (50/53);  new base A (23/23);  total (73/76)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.15e-01

Only 100 of 150 total aligned reads displayed.

TCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGT  >  minE/1933088‑1933223
                                                                   |                                                                    
tcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTc                                                                   >  1:2887221/1‑71 (MQ=255)
tcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTc                                                                   <  1:5644894/71‑1 (MQ=255)
  gtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGc                                                                 >  1:5584112/1‑71 (MQ=255)
   tcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCt                                                                <  1:1432638/71‑1 (MQ=255)
          cGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGcc                                                          <  1:3043267/70‑1 (MQ=255)
          cGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCg                                                         >  1:3763480/1‑71 (MQ=255)
            tCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGt                                                        >  1:5461608/1‑70 (MQ=255)
              tttCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAc                                                     >  1:1110760/1‑71 (MQ=255)
               ttCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGc                                                           >  1:4955044/1‑64 (MQ=255)
               ttCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGt                                                        >  1:1723802/1‑67 (MQ=255)
                tCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAcc                                                    <  1:3059724/70‑1 (MQ=255)
                tCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAc                                                     <  1:3032305/69‑1 (MQ=255)
                  gcgGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCg                                                                  >  1:4927850/1‑54 (MQ=255)
                  gcgGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCg                                                                  >  1:3878992/1‑54 (MQ=255)
                    ggCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt                                               <  1:4699661/71‑1 (MQ=255)
                    ggCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt                                               <  1:234870/71‑1 (MQ=255)
                     ttaaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCAtt                                                       <  1:5163388/60‑1 (MQ=255)
                     ttaaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTc                                              <  1:1364007/69‑1 (MQ=255)
                     ttaaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTc                                              <  1:2611400/69‑1 (MQ=255)
                     gCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTc                                              <  1:1266388/71‑1 (MQ=255)
                      taaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTaaa                                                             <  1:1425217/54‑1 (MQ=255)
                      taaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTaaa                                                             <  1:2442884/54‑1 (MQ=255)
                      cAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCa                                             >  1:5270196/1‑71 (MQ=255)
                       aaCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCAc                                            >  1:701376/1‑71 (MQ=255)
                       aaCCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAg                                                                      >  1:182549/1‑45 (MQ=255)
                       aaCCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            <  1:333592/71‑1 (MQ=255)
                       aaCCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            <  1:5395818/71‑1 (MQ=255)
                        aCCTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCa                                             >  1:3909972/1‑69 (MQ=255)
                         ccTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAcc                                                    <  1:227153/61‑1 (MQ=255)
                          cTGTTCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGac                                         <  1:1620121/71‑1 (MQ=255)
                          cTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGac                                         <  1:5101936/71‑1 (MQ=255)
                            gttCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGacca                                       >  1:410670/3‑71 (MQ=255)
                            gttCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGacca                                       >  1:3179684/3‑71 (MQ=255)
                            gttCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGacca                                       >  1:571443/3‑71 (MQ=255)
                            gttCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGacca                                       >  1:2647253/3‑71 (MQ=255)
                            gttCCTGGAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGacca                                       >  1:5457012/3‑71 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCt                                                                    <  1:5614661/42‑1 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCt                                                                    <  1:1987914/42‑1 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCt                                                                    <  1:5621368/42‑1 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCt                                                                    <  1:2515325/42‑1 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAg                                                            <  1:545302/50‑1 (MQ=255)
                            gATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGacca                                       >  1:3731627/1‑71 (MQ=255)
                             aTCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAcc                                                    <  1:178907/57‑1 (MQ=255)
                              tCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCg                                                         >  1:3529392/1‑51 (MQ=255)
                              tCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGaccac                                      >  1:2465566/1‑70 (MQ=255)
                              tCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGaccac                                      >  1:4423919/1‑70 (MQ=255)
                               ccAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAt                                                 >  1:2960401/1‑58 (MQ=255)
                               ccAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAt                                                 >  1:4631645/1‑58 (MQ=255)
                                ctggAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGaccaccg                                    <  1:2123520/68‑2 (MQ=255)
                                 aGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                  <  1:4794449/71‑1 (MQ=255)
                                 aGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                  <  1:43334/71‑1 (MQ=255)
                                   gAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGc                                                           <  1:4036985/44‑1 (MQ=255)
                                   gAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGaccacc                                     <  1:4235684/66‑1 (MQ=255)
                                   gAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTa                                                      >  1:328915/1‑49 (MQ=255)
                                   gAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATga                                <  1:2335700/71‑1 (MQ=255)
                                   gAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATg                                 <  1:2241059/70‑1 (MQ=255)
                                    aaGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGcc                                                          >  1:2189832/1‑44 (MQ=255)
                                    aaGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt                                               >  1:2858329/1‑55 (MQ=255)
                                     aGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATgaag                              <  1:391826/71‑1 (MQ=255)
                                      gCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt                                               <  1:33644/53‑1 (MQ=255)
                                           gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            >  1:3602863/1‑51 (MQ=255)
                                           gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            >  1:2181999/1‑51 (MQ=255)
                                           gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            >  1:4741048/1‑51 (MQ=255)
                                           gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            >  1:3773649/1‑51 (MQ=255)
                                           gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTc                         >  1:5641659/1‑70 (MQ=255)
                                           cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGaccacc                                     >  1:1547396/3‑58 (MQ=255)
                                           cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGaccacc                                     >  1:1881319/3‑58 (MQ=255)
                                           cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATga                                >  1:4404693/3‑63 (MQ=255)
                                           cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTc                         >  1:1032166/3‑70 (MQ=255)
                                            agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                       <  1:4686757/70‑1 (MQ=255)
                                            agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                       <  1:4362054/70‑1 (MQ=255)
                                             gcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCa                        >  1:1285278/1‑69 (MQ=255)
                                             gcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCa                        >  1:300300/1‑69 (MQ=255)
                                              ccTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATga                                <  1:4215128/60‑1 (MQ=255)
                                               cTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGc                    >  1:1817262/1‑71 (MQ=255)
                                                tGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGaccacc                                     <  1:353530/53‑1 (MQ=255)
                                                tGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTAcc                                                    <  1:2022305/38‑1 (MQ=255)
                                                tGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAt                                                 <  1:1982/41‑1 (MQ=255)
                                                tGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCg                   >  1:3995602/1‑71 (MQ=255)
                                                 gATCTTCTGCGTCGTTTAATTCGCTAAAACCATTAACGATTTCACGACCACCGATGAAGAATTCAAAACgg                  >  1:579612/1‑71 (MQ=255)
                                                 gATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCAc                                            >  1:3852919/1‑45 (MQ=255)
                                                  aTCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGaccaccga                                   >  1:4704987/1‑51 (MQ=255)
                                                  aTCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGt                 >  1:5260041/1‑71 (MQ=255)
                                                    cTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGac                                         >  1:21220/1‑45 (MQ=255)
                                                    cTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTc                >  1:162298/1‑70 (MQ=255)
                                                    cTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCa                                             >  1:3134762/1‑41 (MQ=255)
                                                    cTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCa                                             >  1:2730274/1‑41 (MQ=255)
                                                     ttCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTcgg              >  1:5093520/1‑69 (MQ=255)
                                                     ttCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                   >  1:2649409/1‑50 (MQ=255)
                                                       ccGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGt                 <  1:3795329/66‑1 (MQ=255)
                                                       ccGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCtgt             <  1:148358/70‑1 (MQ=255)
                                                        cgcgTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCtgtg            <  1:5053157/70‑1 (MQ=255)
                                                          cgTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGAtt         <  1:1958619/71‑1 (MQ=255)
                                                            tCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGAttt        <  1:2735161/70‑1 (MQ=255)
                                                              aTTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTcc      <  1:1360530/70‑1 (MQ=255)
                                                               ttCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                   <  1:4072196/40‑1 (MQ=255)
                                                               ttCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                   <  1:687521/40‑1 (MQ=255)
                                                                tCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCggg   >  1:2018706/1‑71 (MQ=255)
                                                                  aGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGt  >  1:5368628/1‑70 (MQ=255)
                                                                  aGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGt  >  1:3826387/1‑70 (MQ=255)
                                                                   |                                                                    
TCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGT  >  minE/1933088‑1933223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A