Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,648,237	G→T	7.0%	W174L (TGG→TTG)	PP_3214 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,648,237	0	G	T	7.0%	180.2 / 3.4	57	W174L (TGG→TTG)	PP_3214	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (25/28);  new base T (2/2);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

GAGAAGGGCGCAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGATCAAGTACGACGTCG  >  NC_002947/3648090‑3648380                                                                                                                                                    |                                                                                                                                                gagaAGGGCGCAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTgg                                                                                                                                                <  6:41762/149‑1 (MQ=255)      gggCGCAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCATCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCAt                                                                                                                                           <  6:31044/149‑1 (MQ=255)      gggCGCAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCAt                                                                                                                                           >  2:27230/1‑149 (MQ=255)        gcgcAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGa                                                                                                                                         >  7:187254/1‑149 (MQ=255)         cgcAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGAc                                                                                                                                        <  2:278086/149‑1 (MQ=255)         cgcAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGAc                                                                                                                                        <  7:76527/149‑1 (MQ=255)              tCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGCATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATAc                                                                                                                                   <  5:257797/149‑1 (MQ=255)                       ccTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTTGGCCATGACGATACCGCTCGGgc                                                                                                                          >  2:251042/1‑149 (MQ=255)                       ccTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTTGGCCATGACGATACCGCTCGGgc                                                                                                                          >  2:256312/1‑149 (MQ=255)                         tGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGgcgc                                                                                                                        >  7:282661/1‑149 (MQ=255)                          gCTTGGGCCCGCTGTCGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCt                                                                                                                       >  3:140265/1‑149 (MQ=255)                           cTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTc                                                                                                                      <  8:252392/149‑1 (MQ=255)                                gCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGa                                                                                                                                         <  6:384050/125‑1 (MQ=255)                                gCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGa                                                                                                                                         >  5:384050/1‑125 (MQ=255)                                  ccGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACAtt                                                                                                               >  3:30863/1‑149 (MQ=255)                                   cGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACAttt                                                                                                              <  7:54710/149‑1 (MQ=255)                                      tGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGa                                                                                                                                         <  1:222493/119‑1 (MQ=255)                                      tGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGa                                                                                                                                         >  2:222493/1‑119 (MQ=255)                                             cTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACgg                                                                                                    >  5:212222/1‑149 (MQ=255)                                                  cctgcctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTTGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCTACGGTTATc                                                                                               <  1:251042/149‑1 (MQ=255)                                                  cctgcctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTTGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATc                                                                                               <  1:256312/149‑1 (MQ=255)                                                     gcctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACAtt                                                                                                               <  8:319843/130‑1 (MQ=255)                                                     gcctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTAGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACAtt                                                                                                               >  7:319843/1‑130 (MQ=255)                                                      cctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTg                                                                                             <  8:282661/147‑1 (MQ=255)                                                       ctgGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAg                                                                                          <  6:363660/149‑1 (MQ=255)                                                          gATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTgg                                                                                       >  3:149629/1‑149 (MQ=255)                                                          gATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTgg                                                                                       <  6:212222/149‑1 (MQ=255)                                                              tGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTAc                                                                                    <  4:149629/148‑1 (MQ=255)                                                                aTCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGt                                                                                  >  7:263087/1‑148 (MQ=255)                                                                  cGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGa                                                                                           >  4:53884/1‑137 (MQ=255)                                                                  cGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGa                                                                                           <  3:53884/137‑1 (MQ=255)                                                                    tttttCACTGAACACTTACTACCGCAAGCCCGATGTGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAatg                                                                             <  4:30863/149‑1 (MQ=255)                                                                          aCTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTgg                                                                       >  5:275436/1‑149 (MQ=255)                                                                            tGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTggg                                                                      >  5:189125/1‑148 (MQ=255)                                                                               acacTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGgcgc                                                                                                                        >  5:324993/1‑95 (MQ=255)                                                                               acacTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGgcgc                                                                                                                        <  6:324993/95‑1 (MQ=255)                                                                                  cTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAg                                                               <  2:332244/149‑1 (MQ=255)                                                                                   ttACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAgg                                                              >  6:142980/1‑149 (MQ=255)                                                                                         ccGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTAc                                                          <  1:27230/147‑1 (MQ=255)                                                                                             aaGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGaa                                                    <  5:142980/149‑1 (MQ=255)                                                                                             aaGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGaa                                                    <  8:187254/149‑1 (MQ=255)                                                                                                         aTCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACATCGAACTATGTAGcc                                          >  7:185595/1‑147 (MQ=255)                                                                                                          tCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGcc                                          >  8:74799/1‑146 (MQ=255)                                                                                                           taCCGGTATAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCggg                                                                                                                           <  2:356220/63‑1 (MQ=255)                                                                                                              cGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGtt                                   <  6:189125/149‑1 (MQ=255)                                                                                                                gTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTc                                 <  7:74799/149‑1 (MQ=255)                                                                                                                gTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTc                                 >  2:287970/1‑149 (MQ=255)                                                                                                                gTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTc                                 <  4:140265/149‑1 (MQ=255)                                                                                                                gTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTc                                 <  1:287970/149‑1 (MQ=255)                                                                                                                     gCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCGATGTCGATCCCGCTCGGTCGCTGCGACATTTTGCTAGACGGTTATCTGGAGTGGTAGGTAAATGATGGGGGTACGAAGGGTACCTCGAACTATGTAGCCGAGAGTTTCGACtg                            >  8:68471/1‑148 (MQ=255)                                                                                                                     gCGTCTGGACAGTCGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTCGAGTGGTACGTCAAAGATCTGCGCACGAAGGGTACCTCGAACTATGTAGCCAATAGTTTCCACt                             >  8:311418/1‑148 (MQ=255)                                                                                                                        tCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAgg                                                              <  8:6491/112‑1 (MQ=255)                                                                                                                             aCAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTAt                                                <  2:290602/121‑1 (MQ=255)                                                                                                                             aCAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTAt                                                >  1:290602/1‑121 (MQ=255)                                                                                                                                gTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGa                 <  8:263087/149‑1 (MQ=255)                                                                                                                                            cccGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGATCAAGTacgacg     >  8:47916/1‑149 (MQ=255)                                                                                                                                              cGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGATCAAGTACGACGTc   >  7:157924/1‑149 (MQ=255)                                                                                                                                               gACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGATCAAGTACGACGTCg  >  5:232483/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                GAGAAGGGCGCAATCGAAAGTACCTGCTTGGGCCCGCTGTTGACCTGAACCTGCCTGGATTTGATCGTTTTTCACTGAACACTTACTACCGCAAGCCCGATGGGATCACCGGTAAAGCGTCTGGACAGTGGCAGATCAACCCGACCTGGGCCATGACGATACCGCTCGGGCGCTCCGACATTTTGCTCGACGGTTATCTGGAGTGGTACGTCAATGATGTGGGGACGAAGGGTACCTCGAACTATGTAGCCAAGAGTTTCCACTTCAACCCCCAGATCAAGTACGACGTCG  >  NC_002947/3648090‑3648380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑