Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,018,260	(A)8→7	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	.	97.1%	303.3 / 2.8	69	coding (308/444 nt)	fliJ	flagellar protein
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base . (36/31);  total (37/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018157‑2018347                                                                                                 |                                                                                               agTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaa                                                                                             >  1:481894/1‑100 (MQ=255)  gTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaa                                                                                            >  2:234811/1‑100 (MQ=255)   tttATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaa                                                                                           >  1:414551/1‑100 (MQ=255)    ttATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaa                                                                                          >  2:2095818/1‑100 (MQ=255)     tATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaac                                                                                         <  2:2148749/100‑2 (MQ=255)       tCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaacaa                                                                                       <  2:1575167/100‑4 (MQ=255)       tCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaacaa                                                                                       >  2:2139014/1‑97 (MQ=255)        ccAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaaaaaacaac                                                                                      <  1:936981/100‑5 (MQ=255)          aGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGt                                                                                   <  2:2204678/100‑1 (MQ=255)              ncTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTAGACATTGCCCTTAACAGTTGGCGAGAAAAAAAA‑AACGTTTg                                                                                >  2:869674/2‑99 (MQ=255)               cTGGAAAAAGCCATTACTCAGCATCGCCAGAAACTTAGTCAGTGGAGGCAGAAAGTTGACAGTGGCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCa                                                                              <  2:1410058/100‑1 (MQ=255)                 ggAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAgg                                                                            >  2:79060/1‑100 (MQ=255)                 ggAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAgg                                                                            >  1:2190830/1‑100 (MQ=255)                 ggAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAgg                                                                            <  2:1664948/100‑1 (MQ=255)                  gAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGc                                                                           >  2:1488772/1‑100 (MQ=255)                   aaaaaGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGcc                                                                          <  1:529401/100‑1 (MQ=255)                       aGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGc                                                                      >  1:1929915/1‑100 (MQ=255)                       aGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGc                                                                      <  2:184416/100‑1 (MQ=255)                        gCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCa                                                                     <  2:164146/100‑1 (MQ=255)                        gCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGAAAAAAA‑AAAAAAAACAACGTTTGCAGGCCTGGCa                                                                     <  1:1161686/100‑1 (MQ=255)                         ccATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAg                                                                    >  2:2204031/1‑100 (MQ=255)                         ccATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAg                                                                    <  2:574634/100‑1 (MQ=255)                          cATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑CAAAACACAACGTTTGCAGGcc                                                                          >  1:18821/1‑93 (MQ=255)                          cATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGa                                                                   >  1:1026441/1‑100 (MQ=255)                              aCTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACt                                                               >  1:246771/1‑100 (MQ=255)                               cTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTg                                                              <  2:2144590/100‑1 (MQ=255)                               cTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTg                                                              >  1:505098/1‑100 (MQ=255)                                 cAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCa                                                            <  2:808588/100‑1 (MQ=255)                                 cAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCa                                                            <  2:981824/100‑1 (MQ=255)                                 cAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCa                                                            >  2:1272701/1‑100 (MQ=255)                                  aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  1:1045554/100‑1 (MQ=255)                                  aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  1:2164314/100‑1 (MQ=255)                                   gCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAgg                                                          >  2:1497207/1‑100 (MQ=255)                                   gCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTGGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAgg                                                          >  2:1567295/1‑100 (MQ=255)                                     aTCGCCAGCAACTTTATCAGTGGACGCAGAAAGTTGACATTGCCTTGAACAGTTGGCGAG‑AAAGAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGaa                                                        >  1:779976/1‑100 (MQ=255)                                       cGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAAc                                                       <  2:414552/99‑1 (MQ=255)                                       cGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACg                                                      <  1:1261405/100‑1 (MQ=255)                                         ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                    >  1:1637918/1‑100 (MQ=255)                                         ccAGCAACTTAACCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACgg                                                     <  1:1234476/99‑1 (MQ=255)                                          cggCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCa                                                   <  1:1402848/98‑1 (MQ=255)                                          cAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCa                                                   >  2:6633/1‑100 (MQ=255)                                                cTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAc                                             >  2:1514964/1‑100 (MQ=255)                                                cTTAATCAGTGGAAGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAc                                             <  2:2116531/100‑1 (MQ=255)                                                   aaTCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggc                                          >  2:349168/1‑100 (MQ=255)                                                   aaTCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggc                                          >  2:1108264/1‑100 (MQ=255)                                                       aGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACggcggcn                                      <  1:342120/100‑2 (MQ=255)                                                          ggACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTg                                   >  2:503598/1‑100 (MQ=255)                                                           gACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGc                                  >  1:2226342/1‑100 (MQ=255)                                                             cGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCtt                                >  2:1019199/1‑100 (MQ=255)                                                                aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             >  1:347987/1‑100 (MQ=255)                                                                aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             <  1:1863202/100‑1 (MQ=255)                                                                  aaaGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             <  1:1862944/98‑1 (MQ=255)                                                                    aGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGaaa                         <  1:1836941/100‑1 (MQ=255)                                                                       tGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAAcc                      <  2:2041516/100‑1 (MQ=255)                                                                       tGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAAcc                      <  2:2040715/100‑1 (MQ=255)                                                                        gACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCg                     >  2:1261662/1‑100 (MQ=255)                                                                          cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                   <  1:2139002/100‑1 (MQ=255)                                                                          cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                   >  2:1905190/1‑100 (MQ=255)                                                                          cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                   <  2:481895/100‑1 (MQ=255)                                                                          cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                   <  2:1637927/100‑1 (MQ=255)                                                                           aTTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCt                  >  2:2071223/1‑100 (MQ=255)                                                                            ttGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTc                 >  1:751351/1‑100 (MQ=255)                                                                             tGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCg                <  2:246771/100‑1 (MQ=255)                                                                              ggccTGAACAGTTAGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGa               >  2:1504253/3‑100 (MQ=255)                                                                              gCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGa               >  1:1581727/1‑100 (MQ=255)                                                                               cccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt              >  1:1062369/1‑100 (MQ=255)                                                                                ccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATc             >  2:1392090/1‑100 (MQ=255)                                                                                ccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATc             <  2:784238/100‑1 (MQ=255)                                                                                ccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATc             <  1:1272699/100‑1 (MQ=255)                                                                                 cTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCa            >  1:1278847/1‑100 (MQ=255)                                                                                   gAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGa          >  2:671742/1‑100 (MQ=255)                                                                                      cAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaaaa       >  1:2148974/1‑100 (MQ=255)                                                                                        gTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAg     >  2:1905420/1‑100 (MQ=255)                                                                                        gTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAg     >  2:1144949/1‑100 (MQ=255)                                                                                          tGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgat   <  1:95582/100‑1 (MQ=255)                                                                                          tGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgat   <  2:1311496/100‑1 (MQ=255)                                                                                           ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgatg  >  2:1794662/1‑100 (MQ=255)                                                                                                 |                                                                                               AGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018157‑2018347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑