Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	638,745	A→T	11.7%	L16Q (CTG→CAG)	PP_0550 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	638,745	0	A	T	11.7%	147.8 / 8.2	51	L16Q (CTG→CAG)	PP_0550	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (20/25);  new base T (3/3);  total (23/28)
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

CCCGCCCGGCCAGTTGCGGAAGGAATACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTACGCAACGC  >  NC_002947/638596‑638881                                                                                                                                                      |                                                                                                                                         cccgcccgGCCAGTTGCGGAAGGAATACCGCCGGGTCGCCGACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCa                                                                                                                                          >  1:1357468/1‑150 (MQ=255) cccgcccgGCCAGTTGCGGAAGGAATACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCa                                                                                                                                          <  2:465627/150‑1 (MQ=255)      ccgGCCAGTTGCGGAAGGAATACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCg                                                                                                                                     <  1:143443/150‑1 (MQ=255)          ccAGTTGCGGAAGGAATACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTgg                                                                                                                                 >  1:1318446/1‑150 (MQ=255)                   gaaggaaTACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCaa                                                                                                                        <  2:906428/150‑1 (MQ=255)                    aaggaaTACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCTGACCGGTgaacacct                                                                                                                           >  1:972258/1‑139 (MQ=255)                    aaggaaTACCGCCGGGTCGCCCACCGGGTTTTCCAGGCGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCTGACCGGTgaacacct                                                                                                                           <  2:972258/146‑8 (MQ=255)                      ggaaTACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCa                                                                                                                     >  1:526779/1‑150 (MQ=255)                       gaaTACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAg                                                                                                                    >  2:771531/1‑150 (MQ=255)                           gtcgctgggTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACa                                                                                                                >  2:1143712/7‑150 (MQ=255)                           aCCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACa                                                                                                                <  2:1098164/150‑1 (MQ=255)                            ccgccgGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGCCAt                                                                                                               >  1:498417/1‑150 (MQ=255)                                    tCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCgg                                                                                                                                    >  1:781333/1‑121 (MQ=255)                                    tCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCgg                                                                                                                                    <  2:781333/121‑1 (MQ=255)                                    tCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGc                                                                                                       <  1:153897/150‑1 (MQ=255)                                    tCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGGGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGc                                                                                                       <  2:372920/150‑1 (MQ=255)                                        ccACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCg                                                                                                                                     >  2:658850/1‑116 (MQ=255)                                        ccACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCg                                                                                                                                     <  1:658850/116‑1 (MQ=255)                                         cACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACCTGCTGAGGCGTCaa                                                                                                  <  2:1090493/150‑1 (MQ=255)                                          aCCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGt                                                                                                                                   >  1:1218047/1‑116 (MQ=255)                                          aCCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGt                                                                                                                                   <  2:1218047/116‑1 (MQ=255)                                              ggTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCGCCGGCAAGCAGGACATGCTGCGCCGTCAAGTACa                                                                                             >  2:110710/1‑150 (MQ=255)                                                  ttCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACatgat                                                                                         <  1:1143712/150‑1 (MQ=255)                                                          gCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTcc                                                                                 <  2:526779/150‑1 (MQ=255)                                                               ccgccGGCCATTGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAgg                                                                                                        >  2:979855/5‑122 (MQ=255)                                                               acgccGGCCATTGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAgg                                                                                                        <  1:979855/118‑1 (MQ=255)                                                                 cTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTa                                                                          <  2:498417/150‑1 (MQ=255)                                                                  tCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTac                                                                         <  2:598844/150‑1 (MQ=255)                                                                  tCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTac                                                                         >  2:1036046/1‑150 (MQ=255)                                                                     gCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACt                                                                      <  2:1318446/150‑1 (MQ=255)                                                                        aaTGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCCGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCaa                                                                   <  1:1079371/150‑1 (MQ=255)                                                                        aaTGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCCGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCaa                                                                   <  1:1079329/150‑1 (MQ=255)                                                                          tGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCa                                                                                                                     <  1:1400329/98‑1 (MQ=255)                                                                          tGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCa                                                                                                                     >  2:1400329/1‑98 (MQ=255)                                                                               ggCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTagt                                                            <  2:141353/150‑1 (MQ=255)                                                                                            cAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCAt                                               >  1:424412/1‑150 (MQ=255)                                                                                                acacGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCAttttt                                           <  2:98591/150‑1 (MQ=255)                                                                                                          tggtggGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCtgcttgc                                 >  1:651306/1‑150 (MQ=255)                                                                                                                          cAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCtgtgt                 <  1:1036046/150‑1 (MQ=255)                                                                                                                                  cTAGCAGGCGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTAc         <  1:771531/150‑1 (MQ=255)                                                                                                                                   tAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCt                                                                                                            <  1:605275/50‑1 (MQ=255)                                                                                                                                   tAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCt                                                                                                            >  2:605275/1‑50 (MQ=255)                                                                                                                                     gCAGGTGTTCACCGGTCAGACCGCAGGCGAGGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTACGCa      >  1:748803/1‑150 (MQ=255)                                                                                                                                       aGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTACGCAAc    >  1:561130/1‑150 (MQ=255)                                                                                                                                         gtgtTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTACGCAAcac  >  1:393389/1‑148 (MQ=255)                                                                                                                                             ccACCGGTCTGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTcc                                                                                 <  2:55199/66‑1 (MQ=255)                                                                                                                                             ccACCGGTCTGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTcc                                                                                 >  1:55199/2‑67 (MQ=255)                                                                                                                                              cACCGGTCTGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCgg                                                   <  2:1036928/96‑1 (MQ=255)                                                                                                                                              cACCGGTCTGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCgg                                                   >  1:1036928/1‑96 (MQ=255)                                                                                                                                                 cGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCtgctt                                   >  2:471940/1‑109 (MQ=255)                                                                                                                                                 cGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCtgctt                                   <  1:471940/109‑1 (MQ=255)                                                                                                                                                    tCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTg                         <  2:1019407/116‑1 (MQ=255)                                                                                                                                                    tCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTg                         >  1:1019407/1‑116 (MQ=255)                                                                                                                                                      |                                                                                                                                         CCCGCCCGGCCAGTTGCGGAAGGAATACCGCCGGGTCGCCCACCGGGTTTTCCAGGTGCGGGTGCTCGGCCAATGGCCGGCGTGTAGGCGCCAGGACACGGGTGATGGTGGGCTCGTTGAGCAGGCGGTCTAGCAGGTGTTCACCGGTCAGACCGGTGGCTCCGGCAAGCAGGACATGCTGAGGCGTCAAGTACATGATGTCTCTCCCTTGTTACACTCAAGTCTAGTGAGTGCCGGGCATTTTTGCCTGCTTGCTCACGTTGGCCTGTGTGGCGTTACGCAACGC  >  NC_002947/638596‑638881

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: ‑