Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,018,260	(A)8→7	100%	coding (315/444 nt)	fliJ →	flagellar protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,018,253	0	A	.	98.6%	318.6 / ‑2.4	70	coding (308/444 nt)	fliJ	flagellar protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (34/35);  total (35/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

GCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018155‑2018347                                                                                                   |                                                                                               gcagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaa                                                                                               >  2:764320/1‑100 (MQ=255)  cagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaa                                                                                              <  1:741790/100‑1 (MQ=255)    gTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaa                                                                                            <  1:1987285/100‑1 (MQ=255)      ttATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaa                                                                                          <  1:2033521/100‑1 (MQ=255)       tATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaac                                                                                         <  2:887652/100‑2 (MQ=255)         tCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaacaa                                                                                       >  1:868747/1‑97 (MQ=255)           cAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACg                                                                                    >  2:2151813/1‑100 (MQ=255)              aCGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAAGTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGttt                                                                                 <  1:1859710/100‑1 (MQ=255)               cGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTg                                                                                >  2:1294037/1‑100 (MQ=255)                gCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGc                                                                               <  2:373458/100‑1 (MQ=255)                  tGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAg                                                                             <  1:84586/100‑1 (MQ=255)                  cggAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAg                                                                             >  2:1961488/2‑100 (MQ=255)                   ggAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAgg                                                                            >  1:2482966/1‑100 (MQ=255)                       aaaGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTg                                                                        <  1:1520655/100‑1 (MQ=255)                       aaaGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTg                                                                        <  1:119300/100‑1 (MQ=255)                       aaaGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTg                                                                        <  2:2463330/100‑1 (MQ=255)                         aGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGc                                                                      <  1:1409410/100‑1 (MQ=255)                          gCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGAAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGc                                                                      <  1:1428634/99‑1 (MQ=255)                           ccATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAg                                                                    <  1:2630206/100‑1 (MQ=255)                           ccATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAg                                                                    >  1:1395811/1‑100 (MQ=255)                           ccATTACTCAGCATCGCCAACAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAg                                                                    >  2:2182702/1‑100 (MQ=255)                            cATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTTGCGAG‑AAACAAACAACGTTTGCAGGCCTGGCAg                                                                    >  2:686972/1‑99 (MQ=255)                            cATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGa                                                                   >  2:686679/1‑100 (MQ=255)                              ttACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGaca                                                                 >  2:1132492/1‑100 (MQ=255)                                aCTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACt                                                               <  2:1283587/100‑1 (MQ=255)                                aCTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACt                                                               >  1:289809/1‑100 (MQ=255)                                  tCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGc                                                             <  2:1140736/100‑1 (MQ=255)                                    aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  1:1226676/100‑1 (MQ=255)                                    aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  2:2423108/100‑1 (MQ=255)                                    aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  1:777576/100‑1 (MQ=255)                                      cATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAgg                                                          <  2:866920/99‑1 (MQ=255)                                        tCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAAc                                                       <  2:1459174/100‑1 (MQ=255)                                        tCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAAc                                                       <  2:289807/100‑1 (MQ=255)                                           ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                    >  2:2592979/1‑100 (MQ=255)                                           ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                    <  1:1472182/100‑1 (MQ=255)                                            cAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                    >  2:1334868/1‑99 (MQ=255)                                             aGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCaa                                                  >  1:926646/1‑100 (MQ=255)                                                aaCTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATcc                                               <  2:1079840/100‑1 (MQ=255)                                                   ttAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAc                                             <  1:2474044/99‑1 (MQ=255)                                                     aaTCAGTGGACGCAGAAAGTTGACATTGCCCTGAATAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggc                                          <  1:324857/100‑1 (MQ=255)                                                      aTCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggcg                                         >  1:2546541/1‑100 (MQ=255)                                                      aTCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggcg                                         <  2:2163065/100‑1 (MQ=255)                                                            ggACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGAAGACACTGCAGGAACGGCAATCCACGGCGGCACt                                    >  1:1179613/1‑100 (MQ=255)                                                            ggACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTg                                   >  2:2158861/1‑100 (MQ=255)                                                              aCGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCt                                 <  2:2595855/100‑1 (MQ=255)                                                               cGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCtt                                >  2:1680269/1‑100 (MQ=255)                                                               cGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCtt                                >  2:1235840/1‑100 (MQ=255)                                                                 cAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGc                              >  2:728709/1‑100 (MQ=255)                                                                 cAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGc                              <  2:2001368/100‑1 (MQ=255)                                                                  aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             >  2:2229992/1‑100 (MQ=255)                                                                  aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             <  2:926637/100‑1 (MQ=255)                                                                     aaGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGaa                          >  1:2206881/1‑100 (MQ=255)                                                                     aaGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCATGGCAGACACTGCAAGAACAGCAATCCACGGCGGCACtcatagaaga                           >  2:2401236/1‑90 (MQ=255)                                                                       gTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGaaaa                        >  2:999531/1‑100 (MQ=255)                                                                         tGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAAcc                      >  2:2051908/1‑100 (MQ=255)                                                                         tGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAAcc                      <  1:2105936/100‑1 (MQ=255)                                                                          gACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACATTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCg                     >  2:1700074/1‑100 (MQ=255)                                                                           aCATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGc                    >  1:836637/1‑100 (MQ=255)                                                                             aTTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCt                  <  1:1961506/100‑1 (MQ=255)                                                                              ttGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTc                 <  2:2120821/100‑1 (MQ=255)                                                                              ttGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTc                 <  1:1805175/100‑1 (MQ=255)                                                                              ttGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGACAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTc                 <  1:1862477/100‑1 (MQ=255)                                                                               tGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCg                >  2:2657877/1‑100 (MQ=255)                                                                                 cccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt              >  1:1888692/1‑100 (MQ=255)                                                                                 cccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt              <  1:1594151/100‑1 (MQ=255)                                                                                   cTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCa            <  1:899545/100‑1 (MQ=255)                                                                                    tGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAg           <  1:1294050/100‑1 (MQ=255)                                                                                    tGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAg           >  2:2368911/1‑100 (MQ=255)                                                                                    tGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATACACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAg           >  1:2119223/1‑100 (MQ=255)                                                                                     gAACAGTTGGCGAG‑AAAAAAACAACTTTTGCAGGCCTTGCAGACACTGCAGGTACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAg           <  2:1473878/99‑1 (MQ=255)                                                                                        cAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaaaa       <  1:1132502/100‑1 (MQ=255)                                                                                          gTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAg     >  1:1306733/1‑100 (MQ=255)                                                                                          gTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAACAGAAAAAg     >  1:2542246/1‑100 (MQ=255)                                                                                             ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgatg  >  2:822680/1‑100 (MQ=255)                                                                                             ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgatg  >  2:2349003/1‑100 (MQ=255)                                                                                             ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgat   >  2:822792/1‑99 (MQ=255)                                                                                                   |                                                                                               GCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018155‑2018347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑