Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,005,131	A→T	11.8%	T495S (ACA→TCA) ‡	PP_4410 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,005,131	0	A	T	11.8%	141.3 / 8.3	58	T495S (ACA→TCA) ‡	PP_4410	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (25/26);  new base T (2/5);  total (27/31)
Fisher's exact test for biased strand distribution p-value = 4.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTAGATTTGGTCTATTTTTGC  >  NC_002947/5004986‑5005278                                                                                                                                                  |                                                                                                                                                    cAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAg                                                                                                                                                  <  1:170363/149‑1 (MQ=255) cAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAg                                                                                                                                                  >  1:254946/1‑149 (MQ=255) cAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAg                                                                                                                                                  >  8:175028/1‑149 (MQ=255) cAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACAAAg                                                                                                                                                  >  7:208768/1‑149 (MQ=255)      aTGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCGTTACGCCTTAAACTCTGCACAACACTATTATTTTGAAAATTCTCTCCGTATATATGAATCTATAGAAAAGGCGCAGCGCCTAAACTCTTACGTCGACAGAGTCTAc                                                                                                                                             >  5:322263/1‑149 (MQ=255)      aTGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGa                                                                                                                                              >  3:69945/1‑148 (MQ=255)         ttttCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgt                                                                                                                                           <  4:243832/148‑3 (MQ=255)           ttCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgtaa                                                                                                                                         <  6:74975/148‑5 (MQ=255)           ttCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTg                                                                                                                                         <  7:175028/148‑1 (MQ=255)             cACCGGAGAGCATCTTCGACAGTTCGTTTCATACCATTACGCCTTAAACGCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACGCTTACGTCGACTGTGTCGAcgtaaga                                                                                                                                       <  3:88673/148‑7 (MQ=255)              aCCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTgggt                                                                                                                                      <  3:225280/148‑3 (MQ=255)              aCCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGAt                                                                                                                                      <  8:88293/148‑1 (MQ=255)                cGGAGAGCAGCTTCGACAGTTCGTTTCTTAGCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTGTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTg                                                                                                                                   <  5:26903/149‑1 (MQ=255)                  gagaGCAGCTTGGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgtaag                                                                                                                                        <  2:56124/142‑6 (MQ=255)                  gagaGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgtaag                                                                                                                                        >  1:56124/1‑137 (MQ=255)                  gagaGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGtt                                                                                                                                 <  1:241104/149‑1 (MQ=255)                           ttCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCAt                                                                                                                         <  1:345501/148‑1 (MQ=255)                                   ttCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgtaaga                                                                                                                                       <  6:315366/126‑7 (MQ=255)                                   ttCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACTGTGTCGAcgtaaga                                                                                                                                       >  5:315366/1‑120 (MQ=255)                                     cGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGaa                                                                                                               <  2:254946/148‑1 (MQ=255)                                     cGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGaa                                                                                                               <  2:259756/148‑1 (MQ=255)                                           ttACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCg                                                                                                                             <  4:235974/128‑1 (MQ=255)                                           ttACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCg                                                                                                                             >  3:235974/1‑128 (MQ=255)                                             aCCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAg                                                                                                         <  2:222351/146‑1 (MQ=255)                                              ccATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATc                                                                                                      <  4:69945/148‑1 (MQ=255)                                                      ccTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATc                                                                                             >  7:152016/1‑149 (MQ=255)                                                      ccTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATc                                                                                             >  6:6154/1‑149 (MQ=255)                                                                tGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACt                                                                                     <  5:6154/147‑1 (MQ=255)                                                                 gcaccaGACTATTATTATGAAAATTCTCTCCTTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCACCTATATCCGAAAACTACa                                                                                  <  4:215586/149‑1 (MQ=255)                                                                   agcagACTATTATTTTGAAAATTCTCTCCGTATATATGATGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATc                                                                                <  8:208768/149‑1 (MQ=255)                                                                          tattatTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACt                                                                          >  3:320513/1‑148 (MQ=255)                                                                                tttGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCa                                                                   >  8:40138/1‑149 (MQ=255)                                                                                           tctcCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTAttt                                                         >  3:216978/1‑148 (MQ=255)                                                                                                gTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTc                                                               >  5:269503/1‑137 (MQ=255)                                                                                                gTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTc                                                               <  6:269503/137‑1 (MQ=255)                                                                                                 tatataTGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATTTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCATATATCACGac                                                   >  5:17778/1‑148 (MQ=255)                                                                                                    atatGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCGCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGactact                                               >  6:172751/1‑149 (MQ=255)                                                                                                      ttGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACAAAGTCGACATTGGATTTGTTCCCGTCATGTACCAAGAAGACAAGATCAGCTATATACGAAAACTAAATAAAGAATCATTTCACATCGTATTTAACGaataatac                                             >  8:213838/2‑145 (MQ=255)                                                                                                       tgtaGCTATAGAAAAGGCGCAGCGGCTCAAGTGTTACGTCGACACATTCGACCTTGTATTTGTTCCCGTCATGTACCACGAAGACTAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCa                                             <  6:17778/145‑1 (MQ=255)                                                                                                       tGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAg                                            >  3:130582/1‑149 (MQ=255)                                                                                                       tGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAg                                            >  3:135664/1‑149 (MQ=255)                                                                                                        gAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGc                                           >  2:325287/1‑149 (MQ=255)                                                                                                           gCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCAt                                                                       >  7:151453/1‑118 (MQ=255)                                                                                                           gCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCAt                                                                       <  8:151453/118‑1 (MQ=255)                                                                                                             tataGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGc                                           >  6:111194/1‑144 (MQ=255)                                                                                                             tataGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGc                                           <  5:111194/144‑1 (MQ=255)                                                                                                              ataGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCAttt                                                                     <  3:252042/117‑1 (MQ=255)                                                                                                              ataGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCAttt                                                                     >  4:252042/1‑117 (MQ=255)                                                                                                                       gcgcAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCgg                            >  8:20384/1‑149 (MQ=255)                                                                                                                        cgcAGCGCCCCAACTCTTACCGCGACACAGTCGACCTTGGATTTGTTCCCGTCCTGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGc                           <  4:74007/149‑1 (MQ=255)                                                                                                                            gcgcCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAAACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCg                       >  4:12510/1‑149 (MQ=255)                                                                                                                               ccTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTa                    <  8:152016/149‑1 (MQ=255)                                                                                                                               ccTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTa                    <  4:216978/149‑1 (MQ=255)                                                                                                                               ccTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTAACACGAAGACAAGATCAGCTATATCCTAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCTTATTACAACCCCGGCTGCGTTa                    <  7:213838/149‑1 (MQ=255)                                                                                                                                 tCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCAAGACTACTCAGCCTATTACAACCCCGGCTGCGt                      >  8:160129/1‑145 (MQ=255)                                                                                                                                          ccGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGATAAGATCATCTATATACGAAAACTACATCCAGACCCATTTCACTTCGTATTTCTCGACTTCTCAGCCTATTTCTACCCCGGCTGCGTTAGATTTGGt            <  6:322263/145‑1 (MQ=255)                                                                                                                                          aCGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTAGATTTgg             <  7:160129/145‑1 (MQ=255)                                                                                                                                              cGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTAGATTTGGTCTAtttt     >  6:179707/1‑149 (MQ=255)                                                                                                                                                 cacaGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTAGATTTGGTCTATTTTTGc  <  4:320513/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CAAAAATGTTTTCACCGGAGAGCAGCTTCGACAGTTCGTTTCTTACCATTACGCCTTAAACTCTGCAGCAGACTATTATTTTGAAAATTCTCTCCGTATATATGAAGCTATAGAAAAGGCGCAGCGCCTCAACTCTTACGTCGACACAGTCGACCTTGGATTTGTTCCCGTCATGTACCACGAAGACAAGATCAGCTATATCCGAAAACTACATCCAGACTCATTTCACTTCGTATTTCACGACTACTCAGCCTATTACAACCCCGGCTGCGTTAGATTTGGTCTATTTTTGC  >  NC_002947/5004986‑5005278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑