Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,470,285	G→T	12.7%	P317T (CCG→ACG)	PP_3961 ←	transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,470,285	0	G	T	12.7%	135.3 / 3.8	46	P317T (CCG→ACG)	PP_3961	transporter
Reads supporting (aligned to +/- strand):  ref base G (19/21);  new base T (2/4);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 6.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCACACATCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAGGACACCGAAC  >  NC_002947/4470141‑4470433                                                                                                                                                 |                                                                                                                                                     cccACACATCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCga                                                                                                                                                 >  2:569273/1‑150 (MQ=255)  ccACACATCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCCCGACCATGATCGTGGCgat                                                                                                                                                <  2:287414/150‑2 (MQ=255)  ccACACATCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCgaa                                                                                                                                                <  2:48526/150‑1 (MQ=255)         tCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAgg                                                                                                                                         >  2:166060/1‑150 (MQ=255)                ccTCCCCAGTTGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCaa                                                                                                                                  <  1:407457/150‑1 (MQ=255)                             tgcGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCCGGACATCCCTATGGACAGTTTGCGGTCTGGCGCGATGCGCTCTACCAGAGGCATGGCCACTAAGATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGAt                                                                                                                     <  1:390660/150‑1 (MQ=255)                              gcGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATg                                                                                                                    <  1:497486/150‑1 (MQ=255)                              gcGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATg                                                                                                                    <  1:45268/150‑1 (MQ=255)                              gcGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATg                                                                                                                    <  1:45264/150‑1 (MQ=255)                                               tCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 <  1:207001/120‑1 (MQ=255)                                               tCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 >  2:207001/1‑120 (MQ=255)                                                          gaCCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCccaccacca                                                                                        <  2:295149/150‑1 (MQ=255)                                                                       ccAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 >  1:407767/1‑96 (MQ=255)                                                                       ccAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 <  2:407767/96‑1 (MQ=255)                                                                       ccAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGGCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGt                                                                           >  1:703976/1‑150 (MQ=255)                                                                          ggTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCAATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGt                                                                        >  1:271019/1‑150 (MQ=255)                                                                              aTCCCTTCGGTAAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGCGGATTACTGCGATCAGCACGGCGATGGACAGCCCGATGATGTTTGTAACGAAGAGGAGCGGGAAGGTTGTcgcc                                                                    >  1:317624/1‑150 (MQ=255)                                                                                  cTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCa                                                                                                                <  1:489712/102‑1 (MQ=255)                                                                                  cTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCa                                                                                                                >  2:489712/1‑102 (MQ=255)                                                                                               gcttTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAacccacc                                                   >  2:473690/1‑150 (MQ=255)                                                                                                cttTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAacccac                                                    >  1:400413/1‑148 (MQ=255)                                                                                                cttTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAacccac                                                    <  2:400413/148‑1 (MQ=255)                                                                                                 tttCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 <  2:98875/70‑1 (MQ=255)                                                                                                 tttCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 >  1:98875/1‑70 (MQ=255)                                                                                                      ggCAAGATCCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGt                                            <  1:596045/150‑1 (MQ=255)                                                                                                       gCACGATGCGCTCTAACCGAAACATCGCCACACACTCTGTCGTGCCGGAGGATATTCCCGCAACCAGCACGGCGATGGCCAGCCCAATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTa                                           <  2:271019/150‑1 (MQ=255)                                                                                                          cGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTagca                                        >  2:224187/1‑150 (MQ=255)                                                                                                           gATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACcag                                                                                       >  2:399446/1‑102 (MQ=255)                                                                                                           gATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACcag                                                                                       <  1:399446/102‑1 (MQ=255)                                                                                                           gATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGGAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTagcag                                       >  1:303380/1‑150 (MQ=255)                                                                                                           gATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTagcag                                       >  2:244690/1‑150 (MQ=255)                                                                                                            aTGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTagcagc                                      <  2:455419/150‑1 (MQ=255)                                                                                                              gcgcTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCtt                                    <  1:166060/150‑1 (MQ=255)                                                                                                              gcgcTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCtt                                    >  2:388036/1‑150 (MQ=255)                                                                                                                 ctctACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 <  1:749809/54‑1 (MQ=255)                                                                                                                 ctctACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAAc                                                                                                                                 >  2:749809/1‑54 (MQ=255)                                                                                                                      ccAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCg                            >  1:86818/1‑150 (MQ=255)                                                                                                                      ccAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCg                            <  1:224187/150‑1 (MQ=255)                                                                                                                       cAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCgg                           <  1:569273/150‑1 (MQ=255)                                                                                                                             cttCGCCCCGACCATGATCGTGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATc                     >  1:319423/3‑150 (MQ=255)                                                                                                                              ttCGCCCCGACCATGATCGTGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAg                                                                             >  2:44180/2‑93 (MQ=38)                                                                                                                              ttCGCCCCGACCATGATCGTGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAg                                                                             <  1:44180/92‑1 (MQ=38)                                                                                                                                     cgaccATGATCGTGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCa             <  2:319423/146‑1 (MQ=255)                                                                                                                                      gATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAg            <  1:473690/150‑1 (MQ=255)                                                                                                                                      gATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAg            <  2:86818/150‑1 (MQ=255)                                                                                                                                        tCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAGGa          >  2:427256/1‑150 (MQ=255)                                                                                                                                                ggggCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAGGACACCGAac  <  2:546369/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     CCCACACATCGACCACCTGCCCAGATGCTGCGGCACCGCCGGCAACTCCAACGTTGAGACCGGCGAGCAACCAGGTCATCCCTTCGGTCAGCTTGCTTTCGGGCACGATGCGCTCTACCAGCGACATCGCCACGATCATGGTCGGGGCGAAGAACAGGCCCGCAACCAGCACGGCGATGGCCAGCCCGATGATGTTTCCCACCACCAGCAGCGGCAAGGTTGTCGCCGCCGTCGCCAACCCACCCAGCAGTAGCAGCTTGTGTAGCGGGGTATCGAGTTTCAGGACACCGAAC  >  NC_002947/4470141‑4470433

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑