Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	196,432	T→C	21.0%	T646T (ACT→ACC)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	196,432	0	T	C	21.0%	79.4 / 8.7	39	T646T (ACT→ACC)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base T (20/9);  new base C (5/3);  total (25/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGT  >  AE015451/196218‑196659                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    aCTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCAt                                                                                                                                                                                                                       >  2:475756/1‑229 (MQ=17) aCTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGCGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAACACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAgt                                                                                                                                                                                                                               >  1:123599/1‑221 (MQ=21)                        aCCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGACTGACGTCTACAACAACGGTTCGACTGTCa                                                                                                                                                                                                                                 >  1:52245/1‑196 (MQ=21)                                                       gcggcgTGATCACTTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAg                                                                                                                                                                                                                                <  2:673964/166‑1 (MQ=255)                                                       gcggcgTGATCACTTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAg                                                                                                                                                                                                                                >  1:673965/1‑166 (MQ=255)                                                                         ccGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACg                                                                                                                                                <  1:511491/228‑1 (MQ=38)                                                                                    aGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCa                                                                                                                                                                                         >  1:590283/1‑176 (MQ=38)                                                                                                 aGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGAcc                                                                                                                                                                                  <  2:541667/170‑1 (MQ=40)                                                                                                 aGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGAcc                                                                                                                                                                                  >  1:541668/1‑170 (MQ=40)                                                                                                      ccGGTAACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGAc                                                                                                                       <  2:447098/224‑1 (MQ=38)                                                                                                                      cagccAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTg                                                                                                                   <  1:504194/209‑1 (MQ=21)                                                                                                                         ccAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCg                                                                                             >  1:624905/1‑231 (MQ=37)                                                                                                                          cAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCgg                                                                                                   >  1:407855/1‑224 (MQ=38)                                                                                                                                    acgaTTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACGGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCAc                                                                             <  1:149145/233‑1 (MQ=9)                                                                                                                                       aTTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTc                                                                                                                                        >  2:504193/1‑174 (MQ=17)                                                                                                                                        ttcccGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCAc                                                                             <  1:159366/229‑1 (MQ=38)                                                                                                                                         tACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTaca                                                                        <  1:606214/236‑1 (MQ=21)                                                                                                                                                 aaGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGAcc                                                                >  1:577764/1‑236 (MQ=18)                                                                                                                                                   gCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGtaag                                                                                >  2:606213/1‑215 (MQ=18)                                                                                                                                                      ggCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAAttt                                                                                                                                                                                               >  2:159365/1‑104 (MQ=40)                                                                                                                                                                          cGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCgg                                                                                                   >  2:392946/1‑176 (MQ=38)                                                                                                                                                                                    aCCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCa                                                                              <  2:590282/187‑1 (MQ=39)                                                                                                                                                                                     ccccGGCGAATGACGTCTACAACAACGGTTCGCCCGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCAGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCgg                                                                                                   >  1:583988/1‑165 (MQ=16)                                                                                                                                                                                         ggCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                                                                                     >  2:21090/1‑175 (MQ=38)                                                                                                                                                                                         ggCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCAc                                                                             >  2:344419/1‑183 (MQ=25)                                                                                                                                                                                         ggCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCAc                                                                             <  1:344420/183‑1 (MQ=25)                                                                                                                                                                                            gAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCa                     >  1:291227/1‑236 (MQ=255)                                                                                                                                                                                             aaTCACGTCTACAACAACGGTTCGACCGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGt                                                                                                      <  1:190411/154‑1 (MQ=18)                                                                                                                                                                                               tGACGTCTACAACAACGGTTCGACGGTCAGCGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                                                                                     <  2:525845/169‑1 (MQ=9)                                                                                                                                                                                                   gTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGa                                                                                                                                                            >  1:472115/1‑94 (MQ=18)                                                                                                                                                                                                     cTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTccc                     >  1:60324/1‑226 (MQ=40)                                                                                                                                                                                                             acGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAAc                   <  2:291226/221‑1 (MQ=40)                                                                                                                                                                                                                 ttCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTg                                                                                                                   >  1:48482/1‑121 (MQ=40)                                                                                                                                                                                                                 ttCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCggtcccc                                                               >  1:468114/1‑167 (MQ=255)                                                                                                                                                                                                                 ttCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCaggtc          >  1:415582/1‑222 (MQ=17)                                                                                                                                                                                                                   cGACTGTCAGTGTGACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCTGCCACTCggacac                                                                                                                                      >  1:397233/1‑96 (MQ=14)                                                                                                                                                                                                                   cGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCCCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGgcggcg                                                                                    >  2:744491/1‑150 (MQ=255)                                                                                                                                                                                                                   cGACCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGt  >  1:22630/1‑232 (MQ=9)                                                                                                                                                                                                                    gACCGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCt                                                                           <  1:231083/158‑1 (MQ=25)                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    ACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGT  >  AE015451/196218‑196659

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑