Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,245,862	(C)6→5	coding (1515/1698 nt)	treA ←	periplasmic trehalase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,245,857	0	C	.	98.2%	229.9 / ‑2.1	56	coding (1520/1698 nt)	treA	periplasmic trehalase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (30/25);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

TGCTGACTTAACGGTCGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCC  >  NC_000913/1245721‑1245990                                                                                                                                         |                                                                                                                                      tGCTGACTTAACGGTCGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGcccc                                                                                                                                    <  2:306098/140‑1 (MQ=255)      aCTTAACGGTCGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGcccccgttc                                                                                                                               <  1:1364711/140‑5 (MQ=255)                cGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGgtggtg                                                                                                                      >  2:1435581/1‑138 (MQ=255)                cGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGgtggtg                                                                                                                      <  1:1435581/138‑1 (MQ=255)                cGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCt                                                                                                                    >  2:208361/1‑140 (MQ=255)                 ggACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTg                                                                                                                   <  1:1054001/140‑1 (MQ=255)                    cgcgTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGAca                                                                                                                <  1:1109833/140‑1 (MQ=255)                                              ttGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTtctc                                                                                      >  2:922731/1‑140 (MQ=255)                                              ttGCTCTTTCGGGCAAATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTtctc                                                                                      <  1:665449/140‑1 (MQ=255)                                                gCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTccc                                                                                    >  1:117470/1‑140 (MQ=255)                                                gCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTccc                                                                                    >  2:16074/1‑140 (MQ=255)                                                gCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTccc                                                                                    <  2:14660/140‑1 (MQ=255)                                                 ctctTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCg                                                                                   >  1:863054/1‑140 (MQ=255)                                                     ttCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCa                                                                               <  2:1050718/140‑1 (MQ=255)                                                      tCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCAt                                                                              >  2:459284/1‑140 (MQ=255)                                                      tCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCAt                                                                              <  1:142038/140‑1 (MQ=255)                                                       cGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATa                                                                             >  1:1111390/1‑140 (MQ=255)                                                        gggCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAg                                                                            >  2:257114/1‑140 (MQ=255)                                                          gCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGgt                                                                          <  2:1111390/140‑1 (MQ=255)                                                               tCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCt                                                                     <  1:16074/140‑1 (MQ=255)                                                                     ccAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACAt                                                               <  2:890677/140‑1 (MQ=255)                                                                             ttCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAgg                                                       >  1:339785/1‑140 (MQ=255)                                                                             ttCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAgg                                                       <  2:1204168/140‑1 (MQ=255)                                                                                  cGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTg                                                  <  2:339785/140‑1 (MQ=255)                                                                                  cGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTg                                                  <  1:743619/140‑1 (MQ=255)                                                                                   gTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGc                                                 >  2:352930/1‑140 (MQ=255)                                                                                         ccATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCt                                            >  2:311773/1‑140 (MQ=255)                                                                                            ttGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATg                                        >  1:1236350/1‑140 (MQ=255)                                                                                             tGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGt                                       >  1:1123316/1‑140 (MQ=255)                                                                                              ggTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTc                                      >  2:702042/1‑140 (MQ=255)                                                                                                   aGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCg                                 <  1:858128/140‑1 (MQ=255)                                                                                                    gCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGc                                >  2:835335/1‑140 (MQ=255)                                                                                                      cAAAGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCa                              <  1:459284/140‑1 (MQ=255)                                                                                                       aaaGCCATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCAc                             <  1:702042/140‑1 (MQ=255)                                                                                                            cATCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCtt                        <  2:614133/140‑1 (MQ=255)                                                                                                              tCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCtttt                      >  1:1353481/1‑140 (MQ=255)                                                                                                              tCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCtttt                      >  1:632538/1‑140 (MQ=255)                                                                                                              tCCTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCtttt                      >  1:1368055/1‑140 (MQ=255)                                                                                                               ccTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCttttt                     >  2:784515/1‑140 (MQ=255)                                                                                                               ccTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCttttt                     <  2:632538/140‑1 (MQ=255)                                                                                                               ccTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCttttt                     <  1:1256843/140‑1 (MQ=255)                                                                                                               ccTGTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCttttt                     >  2:973901/1‑140 (MQ=255)                                                                                                                  gTAATGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGcc                  <  1:1235368/140‑1 (MQ=255)                                                                                                                      tGGATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCATa              <  2:863054/140‑1 (MQ=255)                                                                                                                       ggATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGTACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAg             <  1:768811/140‑1 (MQ=255)                                                                                                                        gATATTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGt            >  1:600190/1‑140 (MQ=255)                                                                                                                         atatTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGtt           <  2:1123316/140‑1 (MQ=255)                                                                                                                          tatTCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGttt          >  2:420152/1‑140 (MQ=255)                                                                                                                             tCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCg                >  2:798497/1‑131 (MQ=255)                                                                                                                             tCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCg                <  1:798497/131‑1 (MQ=255)                                                                                                                             tCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGttt          >  1:340966/1‑137 (MQ=255)                                                                                                                             tCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGttt          <  2:340966/137‑1 (MQ=255)                                                                                                                             tCGCCACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGt       >  1:1314925/1‑140 (MQ=255)                                                                                                                                ccACCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCGGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAAt    >  1:1149259/1‑140 (MQ=255)                                                                                                                                  aCCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATcc  >  2:35691/1‑140 (MQ=255)                                                                                                                                  aCCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATcc  >  2:1373387/1‑140 (MQ=255)                                                                                                                                  aCCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATcc  >  2:1160784/1‑140 (MQ=255)                                                                                                                                  aCCGCCG‑CCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATcc  >  1:310252/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                      TGCTGACTTAACGGTCGGACGCGTCGCCGGAACATTGTCACACGGTTGCTCTTTCGGGCAGATCAAATCCAGCATTTTCAGCGTCACGCCATTGGTCCAGCCAAAGCCATCCTGTAATGGATATTCGCCACCGCCGCCCCCCGTTCCGGTGGTGCTGACATCATATTTTTCCACCAGCTTTTTCTCCCGGTCATAGGTGTGCTGAACATTGGTCAGGAAGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCC  >  NC_000913/1245721‑1245990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑