Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,490,156	C→A	9.3%	L584F (TTG→TTT)	PP_3982 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,490,156	0	C	A	9.3%	152.0 / 2.4	50	L584F (TTG→TTT)	PP_3982	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/20);  new base A (2/3);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCGTCCTCGCGCCCCACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACTCACCAA  >  NC_002947/4490010‑4490304                                                                                                                                                   |                                                                                                                                                     cGGCGTCCTCGCGCCAAACGGAAGCAGAGTTCTATTCGAACTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAAt                                                                                                                                                   >  2:785861/1‑150 (MQ=255)       ccTCGCGCCCCACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCa                                                                                                                                             <  1:1121350/150‑1 (MQ=255)       ccTCGCGCCCCACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCa                                                                                                                                             <  2:506981/150‑1 (MQ=255)        cTCGCGCCCCACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCaa                                                                                                                                            >  2:727480/1‑149 (MQ=255)                ccACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATAAATGTGCCAGGCAACTCg                                                                                                                                    >  1:366929/1‑150 (MQ=255)                       aGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGAt                                                                                                                             <  2:984928/150‑1 (MQ=255)                          agagTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGcc                                                                                                                          >  2:91892/1‑150 (MQ=255)                              ttCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCg                                                                                                                      >  1:1043406/1‑150 (MQ=255)                               tCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTACGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGc                                                                                                                     >  2:827117/1‑150 (MQ=255)                                 tATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGcac                                                                                                                   >  2:335651/1‑149 (MQ=255)                                     cGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGTTCCAATGCTTGCGCGTCGATTTCAGCCATCAATGTGCCAGGCAACTCGGTTCGATGCCTTCGCAACAAg                                                                                                               <  2:155602/150‑1 (MQ=255)                                               cAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACt                                                                                                     >  2:747406/1‑150 (MQ=255)                                               cAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGATGCAAAAGTTGTAGAGATATTAGGCTATCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACt                                                                                                     >  1:135531/1‑150 (MQ=255)                                                 gTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCg                                                                                                   <  2:844805/150‑1 (MQ=255)                                                 gTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCAATGCATATCGCACGTTTATCTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCg                                                                                                   <  1:917503/150‑1 (MQ=255)                                                  ttAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCgg                                                                                                  <  2:129725/150‑1 (MQ=255)                                                       ggCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATaa                                                                                             <  1:915243/150‑1 (MQ=255)                                                        gCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTACGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAg                                                                                            <  1:827117/150‑1 (MQ=255)                                                                    cAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTc                                                                                <  1:54932/150‑1 (MQ=255)                                                                    cAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTc                                                                                <  1:1109923/150‑1 (MQ=255)                                                                     aGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCg                                                                               >  1:1095779/1‑150 (MQ=255)                                                                     aGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATAAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCg                                                                               >  1:133427/1‑150 (MQ=255)                                                                        gAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCAc                                                                            <  2:1043406/150‑1 (MQ=255)                                                                               tCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCg                                                                     <  1:421213/150‑1 (MQ=255)                                                                                 ttCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCATCTCAGCGGc                                                                   >  1:55102/1‑150 (MQ=255)                                                                                 ttCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGc                                                                   >  1:1031507/1‑150 (MQ=255)                                                                                    ctctGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAAt                                                                >  1:819420/1‑150 (MQ=255)                                                                                            ctcGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCg                                                                                                   <  1:698837/107‑1 (MQ=255)                                                                                            ctcGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCg                                                                                                   >  2:698837/1‑107 (MQ=255)                                                                                             tcGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTcgcg                                                       >  2:454851/1‑150 (MQ=255)                                                                                              cGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCgcgc                                                      <  2:1095779/150‑1 (MQ=255)                                                                                                       aaCTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCgg                                                                                                  >  1:336035/1‑97 (MQ=255)                                                                                                       aaCTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCgg                                                                                                  <  2:336035/97‑1 (MQ=255)                                                                                                        aCTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTAcagcag                                            >  2:139098/1‑150 (MQ=255)                                                                                                               gTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGc                                     >  1:657684/1‑150 (MQ=255)                                                                                                               gTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGc                                     >  1:427243/1‑150 (MQ=255)                                                                                                               gTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGc                                     <  2:657684/150‑1 (MQ=255)                                                                                                                               tGCGCGTTCAAGCCGGCCATAAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAATACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTc                     <  2:366929/150‑1 (MQ=255)                                                                                                                                gcgcGTTCAAGCCGGCCATAAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCt                    <  2:133427/150‑1 (MQ=255)                                                                                                                                   cgTTCAAGCCGGCCATACGTGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCa                 <  1:335651/150‑1 (MQ=255)                                                                                                                                    gTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACCGCAGCCGCTGCGCTCAGCACAGCGTTCTGCAc                >  2:787685/1‑150 (MQ=255)                                                                                                                                    gTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCAc                >  1:884429/1‑150 (MQ=255)                                                                                                                                     ttCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCAcc               >  1:58515/1‑150 (MQ=255)                                                                                                                                        aaGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCg            >  1:314200/1‑150 (MQ=255)                                                                                                                                            cGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACt        >  2:1090659/1‑150 (MQ=255)                                                                                                                                            cGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACt        <  2:980268/150‑1 (MQ=255)                                                                                                                                              gCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGACCTCa      <  2:884429/150‑1 (MQ=255)                                                                                                                                               ccATCAATGTGCCAGGCAACTCGGATCGATGCCTTCTCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACTCAc     <  2:819420/150‑1 (MQ=255)                                                                                                                                                cATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACTCAcc    >  1:123233/1‑150 (MQ=255)                                                                                                                                                  tCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACTCACCaa  >  1:277358/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                     CGGCGTCCTCGCGCCCCACGGAAGCAGAGTTCTATTCGACCTTCACCAGTTAATGGCAGGTGCAGTTCAGCGAGTTTGTCTTCCTCTGCATCTCGCACGTTGAACTCGTTGTAGAGATCCAATGCTTGCGCGTTCAAGCCGGCCATCAATGTGCCAGGCAACTCGGATCGATGCCTTCGCAACAAGGCCAAAAACTCGGCATAAGCCGCCTGGATTCGCACCTCAGCGGCAATCAGGTCGCGCTCTACAGCAGCCGCTGCGATCAGCACAGCGTTCTGCACCTCGAACTCACCAA  >  NC_002947/4490010‑4490304

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: ‑