Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,411,662	A→T	10.0%	N59I (AAT→ATT)	PP_5551 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,411,662	0	A	T	10.0%	128.4 / 3.8	48	N59I (AAT→ATT)	PP_5551	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (22/20);  new base T (2/2);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

ATTGCACTTGTCCTGTCTGTTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCT  >  NC_002947/3411514‑3411809                                                                                                                                                      |                                                                                                                                                    aTTGCACTTGTCCTGTCTGTTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCaa                                                                                                                                                     >  7:202764/1‑149 (MQ=255)       cTTGTCCTGTCTGTTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCaa                                                                                                                                               <  7:334453/149‑1 (MQ=255)               gtctgtTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGATTGACCTTCGCAAGCtc                                                                                                                                           >  6:204159/1‑144 (MQ=255)               gtctgtTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGATTGACCTTCGCAAGCtc                                                                                                                                           <  5:204159/145‑2 (MQ=255)                   gttgtAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGATTGACCTTCGCAAGCt                                                                                                                                            >  4:226462/1‑140 (MQ=255)                   gttgtAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGATTGACCTTCGCAAGCt                                                                                                                                            <  3:226462/140‑1 (MQ=255)                    ttgtAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGa                                                                                                                                   >  5:186481/1‑148 (MQ=255)                      gtAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGaaa                                                                                                                                 <  6:77146/148‑1 (MQ=255)                       tAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCtt                                                                                                                                      <  8:157696/142‑1 (MQ=255)                       tAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCtt                                                                                                                                      >  7:157696/1‑142 (MQ=255)                         aCGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGa                                                                                                                              <  4:313077/148‑1 (MQ=255)                          cGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGAtt                                                                                                                            <  7:308259/149‑1 (MQ=255)                           gCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTa                                                                                                                           <  3:331609/149‑1 (MQ=255)                               gTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTc                                                                                                                        >  1:34737/1‑148 (MQ=255)                                   cTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACt                                                                                                                         <  4:305924/143‑1 (MQ=255)                                   cTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACt                                                                                                                         >  3:305924/1‑143 (MQ=255)                                                       cGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGt                                                                                               <  5:226146/149‑1 (MQ=255)                                                          tCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCAc                                                                                            >  5:28316/1‑149 (MQ=255)                                                              cGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCActct                                                                                         <  6:186481/148‑1 (MQ=255)                                                                   gATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGAGTCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGa                                                                                                                              >  1:248280/1‑107 (MQ=255)                                                                   gATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGa                                                                                                                              <  2:248280/106‑1 (MQ=255)                                                                         gCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCATAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGAc                                                                             >  8:79828/1‑149 (MQ=255)                                                                         gCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCATGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGAc                                                                             >  6:324957/1‑149 (MQ=255)                                                                           tAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGa                                                                           >  2:309250/1‑149 (MQ=255)                                                                              tttAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGt                                                                         >  4:659/1‑148 (MQ=255)                                                                                      gTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGt                                                                <  6:28316/149‑1 (MQ=255)                                                                                       tCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTg                                                               <  3:659/149‑1 (MQ=255)                                                                                          ggCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAgg                                                            <  2:34737/149‑1 (MQ=255)                                                                                                     a‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTTCTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTcc                                                 <  5:359228/149‑1 (MQ=255)                                                                                                           gAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCtt                                            >  4:227788/1‑149 (MQ=255)                                                                                                           gAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCtt                                            >  1:190929/1‑149 (MQ=255)                                                                                                              gATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGAt                                         <  7:29566/149‑1 (MQ=255)                                                                                                                   aaaGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAg                                                             <  1:18283/124‑1 (MQ=255)                                                                                                                   aaaGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAg                                                             >  2:18283/1‑124 (MQ=255)                                                                                                                   aaaGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTa                                     >  2:324644/1‑148 (MQ=255)                                                                                                                    aaGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGa                                          <  5:271591/142‑1 (MQ=255)                                                                                                                    aaGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGa                                          >  6:271591/1‑142 (MQ=255)                                                                                                                                 aagaagAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAg                      >  7:124022/1‑149 (MQ=255)                                                                                                                                    aagaGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGAc                   >  1:151152/1‑149 (MQ=255)                                                                                                                                     agagCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGAc                   <  1:324644/148‑1 (MQ=255)                                                                                                                                      gagCTTGCGAAGGTCAGTCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCt                 >  8:338375/1‑149 (MQ=255)                                                                                                                                       agCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCtt                >  4:367157/1‑149 (MQ=255)                                                                                                                                        gCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCttt               >  6:219450/1‑149 (MQ=255)                                                                                                                                         cTTGCGAAGGTCAGTCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTc              <  7:338375/149‑1 (MQ=255)                                                                                                                                          ttGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCg             >  2:340183/1‑149 (MQ=255)                                                                                                                                            gCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCgg            >  6:278826/1‑148 (MQ=255)                                                                                                                                              gAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCGGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGAACCTTTCGGc           >  1:319208/1‑147 (MQ=255)                                                                                                                                                 ggTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGAt      <  8:202764/149‑1 (MQ=255)                                                                                                                                                   tCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGt    <  1:340183/149‑1 (MQ=255)                                                                                                                                                     aaTCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCt  <  2:190929/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    ATTGCACTTGTCCTGTCTGTTGTAACGCTGGTCGCTCAGAATAAGCAAAGCAAGCGATCTGCGGCTGATCAGGCTAATTTAGCAAGTCAGGCCGCGAGGGA‑TCGTGAAGATCTAAAGAATTCTGCAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCT  >  NC_002947/3411514‑3411809

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: ‑