Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,614,798	A→G	8.5%	Q390R (CAG→CGG)	PP_4085 →	rhs family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,614,798	0	A	G	8.5%	127.8 / 2.9	47	Q390R (CAG→CGG)	PP_4085	rhs family protein
Reads supporting (aligned to +/- strand):  ref base A (20/23);  new base G (2/2);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.12e-01

CCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACCTGCTGTACGACGAACA  >  NC_002947/4614651‑4614945                                                                                                                                                     |                                                                                                                                                    ccTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAg                                                                                                                                                    >  8:163259/1‑149 (MQ=255)      gAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTg                                                                                                                                                 >  5:132050/1‑147 (MQ=255)       aaGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTgga                                                                                                                                               <  1:100735/148‑1 (MQ=255)       aaGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTgga                                                                                                                                               <  7:181836/148‑1 (MQ=255)          tGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGAc                                                                                                                                           >  2:252789/1‑149 (MQ=255)             aGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGc                                                                                                                                        <  3:51209/149‑1 (MQ=255)                       cgTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGtt                                                                                                                               >  6:139974/1‑148 (MQ=255)                       cgTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGtt                                                                                                                               <  5:139974/148‑1 (MQ=255)                       cgTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTg                                                                                                                              <  3:18866/149‑1 (MQ=255)                       cgTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTg                                                                                                                              <  3:75650/149‑1 (MQ=255)                         tCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTc                                                                                                                            >  2:269490/1‑149 (MQ=255)                           ccAAATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGTCGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCCTCCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCg                                                                                                                           <  1:252789/149‑1 (MQ=255)                                   tCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATc                                                                                                                   >  6:220276/1‑148 (MQ=255)                                          ggTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAgg                                                                                                           <  7:163259/149‑1 (MQ=255)                                           gTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAggg                                                                                                          <  6:169464/149‑1 (MQ=255)                                                  gtgGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATc                                                                                                   <  4:250417/149‑1 (MQ=255)                                                    ggATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCgg                                                                                                 <  6:248323/149‑1 (MQ=255)                                                       tCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTc                                                                                              >  3:199995/1‑149 (MQ=255)                                                            aTCGACAACGACGGTAACCGACTTGAACTGGGCCGCCTCAGTGACGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGa                                                                                         <  1:182644/149‑1 (MQ=255)                                                            aTCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGa                                                                                         >  4:313659/1‑149 (MQ=255)                                                            aTCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGa                                                                                         <  1:16133/149‑1 (MQ=255)                                                                    cgacgGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGTCCTTCTTCCAGATGGAGGACGGCCAGACCGTTGTCGAAGATAGCAATGAAGGGCTTTATCGGGTCTTCGATACCGAcc                                                                                 >  6:72595/1‑149 (MQ=255)                                                                        ggTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCt                                                                             <  4:226277/149‑1 (MQ=255)                                                                                  tGGATCTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCGGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCtt                                                                                            <  6:94091/124‑1 (MQ=255)                                                                                  tGGATCTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCGGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCtt                                                                                            >  5:94091/1‑124 (MQ=255)                                                                                  tGGATCTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCGGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCtt                                                                                            >  5:98651/1‑124 (MQ=255)                                                                                  tGGATCTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCGGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCtt                                                                                            <  6:98651/124‑1 (MQ=255)                                                                                        tGGGCCGCCTCAGTGCCGGTGAGGCCTACAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCa                                                             >  7:49140/1‑149 (MQ=255)                                                                                            ccgccTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGc                                                         >  3:3647/1‑149 (MQ=255)                                                                                               ccTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGa                                                      <  5:220276/149‑1 (MQ=255)                                                                                               ccTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGa                                                      <  1:269490/149‑1 (MQ=255)                                                                                                           tGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCg                                          <  3:72969/149‑1 (MQ=255)                                                                                                               gCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGAcc                                       <  3:97522/148‑1 (MQ=255)                                                                                                                 cTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGc                                     >  3:203012/1‑148 (MQ=255)                                                                                                                    cat‑caGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCaa                                   <  3:150378/147‑1 (MQ=255)                                                                                                                    cat‑caGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAAt                                  <  6:132050/148‑1 (MQ=255)                                                                                                                          gTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAAt                            >  7:283498/1‑149 (MQ=255)                                                                                                                           tGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAAtt                           >  1:154671/1‑149 (MQ=255)                                                                                                                                     ggCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACct                 >  6:272253/1‑149 (MQ=255)                                                                                                                                     ggCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACct                 >  3:241292/1‑149 (MQ=255)                                                                                                                                        ttGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCa                                                             >  6:192710/1‑102 (MQ=255)                                                                                                                                        ttGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCa                                                             <  5:192710/102‑1 (MQ=255)                                                                                                                                           gCCGTCCTCCAGCTGGATGAAGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACCTGCTGTa           >  4:298174/1‑149 (MQ=255)                                                                                                                                             cttcttCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCaa                             >  6:133156/1‑129 (MQ=255)                                                                                                                                             cttcttCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCaa                             <  5:133156/129‑1 (MQ=255)                                                                                                                                             cttcttCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACCTGCTGTac          >  4:76130/1‑148 (MQ=255)                                                                                                                                                    cAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACCTGCTGTACGACGAACa  <  8:283498/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTACGCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCAT‑CAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGACCCGCTGAATCCGAAACGCTCACGGCTGATCAGGCTCGGCGACCGCAATCTCAATTGCCTCGACCTGCTGTACGACGAACA  >  NC_002947/4614651‑4614945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑