Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,033,085	A→C	7.2%	M227L (ATG→CTG)	PP_3555 →	transmembrane sensor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,033,085	0	A	C	7.2%	150.7 / 4.7	56	M227L (ATG→CTG)	PP_3555	transmembrane sensor
Reads supporting (aligned to +/- strand):  ref base A (28/24);  new base C (2/2);  total (30/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.33e-01

GGCAGTGGCCAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCTACC  >  NC_002947/4032947‑4033229                                                                                                                                           |                                                                                                                                                 ggCAGTGGCCAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCCCCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGc                                                                                                                                       >  2:1010929/1‑150 (MQ=255)  gCAGTGGCCAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCt                                                                                                                                      >  2:464709/1‑150 (MQ=255)       ggCCAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCCTGCATGCCAgggccaag                                                                                                                                 <  1:62795/150‑8 (MQ=255)         ccAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACaa                                                                                                                               >  2:786981/1‑150 (MQ=255)           aGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAgg                                                                                                                             <  1:826355/150‑1 (MQ=255)           aGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGCACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAgg                                                                                                                             <  2:1028969/150‑1 (MQ=255)                      aCCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACAGCCTTGGCCCTAGCATGCGGGGCTGCTACCACAAGACCGACTTCGaa                                                                                                                  >  2:1374548/1‑149 (MQ=255)                        cGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGc                                                                                                                           <  1:1271723/139‑1 (MQ=255)                        cGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGc                                                                                                                           >  2:1271723/1‑139 (MQ=255)                          gCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGCCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGc                                                                                                              <  2:613105/150‑1 (MQ=255)                              ccAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCt                                                                                                          <  2:1245885/150‑1 (MQ=255)                                  ttCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAg                                                                                                      >  1:782739/1‑150 (MQ=255)                                     aaCGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCaa                                                                                                   >  1:1322745/1‑150 (MQ=255)                                      aCGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCaaa                                                                                                  <  1:1374548/150‑1 (MQ=255)                                                gTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTa                                                                                                                                     <  2:599383/105‑1 (MQ=255)                                                gTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTa                                                                                                                                     >  1:599383/1‑105 (MQ=255)                                                 tACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTAt                                                                                       <  2:189791/150‑1 (MQ=255)                                                        accaggTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACa                                                                                <  1:786981/150‑1 (MQ=255)                                                         ccaggTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAg                                                                               >  2:674269/1‑150 (MQ=255)                                                              tGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTgg                                                                          >  2:803060/1‑150 (MQ=255)                                                                  ggTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGAc                                                                                                                        <  2:802310/100‑1 (MQ=255)                                                                  ggTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGAc                                                                                                                        >  1:802310/1‑100 (MQ=255)                                                                  ggTCACCCCGGCTGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCCCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGTCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATg                                                                      <  1:513488/150‑1 (MQ=255)                                                                    tCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGgc                                                                    >  1:1389229/1‑150 (MQ=255)                                                                       cccTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCa                                                                 <  1:899078/150‑1 (MQ=255)                                                                        ccTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCCTGCATGcc                                                                                                                                          >  2:51541/1‑76 (MQ=255)                                                                        ccTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCCTGCATGcc                                                                                                                                          <  1:51541/76‑1 (MQ=255)                                                                        ccTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAACGCGACGACTATGGCAACAGCCTGGCATGGCGCAg                                                                >  2:71867/1‑150 (MQ=255)                                                                        ccTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAg                                                                >  1:1299929/1‑150 (MQ=255)                                                                         cTGGTGGACGGTTCAGTGCTAGTGGGCAGTGTGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCAAGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGc                                                               <  1:1380882/150‑1 (MQ=255)                                                                            gtggAATGTTCGGTACTGGTGTCCAGTTAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGc                                                            >  2:1124159/1‑150 (MQ=255)                                                                             tggAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCa                                                           >  1:1395470/1‑150 (MQ=255)                                                                               gAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAg                                                         >  2:73358/1‑150 (MQ=255)                                                                                     tCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAgg                                                                                                                             <  2:187106/76‑1 (MQ=255)                                                                                     tCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAgg                                                                                                                             >  1:187106/1‑76 (MQ=255)                                                                                      cAGTGCTGGTGTCCAGTGAGGGCAGTTCTGGTGGCTACCGCATTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGc                                                  <  1:575626/150‑1 (MQ=255)                                                                                         tGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATg                                                                      >  1:528968/1‑127 (MQ=255)                                                                                         tGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATg                                                                      <  2:528968/127‑1 (MQ=255)                                                                                         tGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTcc                                               >  2:1071262/1‑149 (MQ=255)                                                                                            tGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACa                                            >  1:1061897/1‑150 (MQ=255)                                                                                             ggTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACaa                                           <  1:1124159/150‑1 (MQ=255)                                                                                              gtgtCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAAc                                          <  2:1389229/150‑1 (MQ=255)                                                                                                   cAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAg                                     >  1:395888/1‑150 (MQ=255)                                                                                                      ggAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCt                                  <  2:438217/149‑1 (MQ=255)                                                                                                       gAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTg                                 <  1:73358/150‑1 (MQ=255)                                                                                                                       gCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCgg                 <  2:395888/150‑1 (MQ=255)                                                                                                                         tACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTg               >  2:1110095/1‑150 (MQ=255)                                                                                                                         tACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTg               >  1:1349343/1‑150 (MQ=255)                                                                                                                          aCCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGa              <  2:1322745/150‑1 (MQ=255)                                                                                                                           ccGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATg                                                                                      >  2:1106045/1‑77 (MQ=255)                                                                                                                           ccGCCTTGGCCCTGGCATGCAGGCCACCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATg                                                                                      <  1:1106045/77‑1 (MQ=255)                                                                                                                               cTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAAc         <  1:803060/150‑1 (MQ=255)                                                                                                                                   tagcTGGCCTGCATGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCt     >  2:139085/4‑150 (MQ=255)                                                                                                                                   gCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCt     >  1:41619/1‑150 (MQ=255)                                                                                                                                    cccTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCTa    >  1:480204/1‑150 (MQ=255)                                                                                                                                      cTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCTAcc  >  1:1151600/1‑150 (MQ=255)                                                                                                                                           aTGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCgg                 >  2:951947/1‑130 (MQ=255)                                                                                                                                           aTGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCgg                 <  1:951947/130‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                 GGCAGTGGCCAGACCCGGGTCACCGGCACCCAGTTCAACGTGTGGAAGTACCAGGACCAGGTGAAGGTCACCCTGGTGGAAGGTTCAGTGCTGGTGTCCAGTGAGGGCAGTGCCGGTGGCTACCGCCTTGGCCCTGGCATGCAGGCCAGCTACCACAAGGGCGACTTCGAGCCGCAGCTGGAGCAAAGCGACGACTATGGCAACAGCCTGGCATGGCGCAGCGGCAAGCTGGTGCTCGACAACCTGAGCCTGGAACAGGCGCTGCCGGTGATCAACCGCTACC  >  NC_002947/4032947‑4033229

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: ‑