Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,614,721	C→T	8.3%	D364D (GAC→GAT)	PP_4085 →	rhs family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,614,721	0	C	T	8.3%	132.4 / 2.3	48	D364D (GAC→GAT)	PP_4085	rhs family protein
Reads supporting (aligned to +/- strand):  ref base C (23/21);  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 = 1.60e-01

ATCCAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGA  >  NC_002947/4614578‑4614864                                                                                                                                                 |                                                                                                                                                aTCCAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACgg                                                                                                                                               <  3:29733/146‑1 (MQ=255) aTCCAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACgg                                                                                                                                               >  4:29733/1‑146 (MQ=255) aTCCAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTaa                                                                                                                                            >  8:233170/1‑149 (MQ=255)    cAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGGGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAAcc                                                                                                                                          <  4:171745/148‑1 (MQ=255)                 gcTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGgc                                                                                                                            >  8:285121/1‑149 (MQ=255)                   tACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGgccg                                                                                                                          >  1:49957/1‑149 (MQ=255)                         agcagGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAg                                                                                                                    >  2:254074/1‑149 (MQ=255)                              ggACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCg                                                                                                               >  1:352119/1‑149 (MQ=255)                                     cgcTGCGACGGTCTAGTGGGGATGGGTTGGAGTGTCCCCTTTGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGTATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGc                                                                                                        <  5:245375/149‑1 (MQ=255)                                          cGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTtca                                                                                                   >  4:136070/1‑149 (MQ=255)                                             cGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTtcatca                                                                                                <  1:254074/149‑1 (MQ=255)                                                tCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTg                                                                                             >  5:55796/1‑149 (MQ=255)                                                tCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTg                                                                                             >  5:11215/1‑149 (MQ=255)                                                ccTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTg                                                                                             <  1:309465/148‑1 (MQ=255)                                                       gggATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCTGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGa                                                                                      <  2:49957/149‑1 (MQ=255)                                                       gggATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTg                                                                                        <  2:302565/147‑1 (MQ=255)                                                                       tCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCttcttc                                                                      <  1:204163/149‑1 (MQ=255)                                                                          ccTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAg                                                                   >  7:254068/1‑149 (MQ=255)                                                                           cTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTg                                                                                                                                     <  3:207047/82‑1 (MQ=255)                                                                           cTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTg                                                                                                                                     >  4:207047/1‑82 (MQ=255)                                                                           cTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGc                                                                  >  6:137312/1‑149 (MQ=255)                                                                                 aGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTggag                                                             <  6:55796/148‑1 (MQ=255)                                                                                        cTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCa                                                     <  7:285121/149‑1 (MQ=255)                                                                                         tGGCCCGCGTCCCACATCCTCAAGGCGGTACGGCTGTGGATCTACATCGACAACGATGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGc                                                       >  1:226084/1‑147 (MQ=255)                                                                                           gCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTCGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGAc                                                  >  4:313509/1‑149 (MQ=255)                                                                                             ccGCGTCCCACATCCTCAAGGTGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCg                                                >  5:72086/1‑149 (MQ=255)                                                                                             ccGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGAt                                                                                                          <  4:46423/91‑1 (MQ=255)                                                                                             ccGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGAt                                                                                                          >  3:46423/1‑91 (MQ=255)                                                                                                  tCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGATGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTc                                           <  2:226084/149‑1 (MQ=255)                                                                                                    ccACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGa                                         <  2:352119/149‑1 (MQ=255)                                                                                                      acaTCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCa                                                                    <  5:2068/120‑1 (MQ=255)                                                                                                      acaTCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCa                                                                    >  6:2068/1‑120 (MQ=255)                                                                                                      acaTCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCg                                          >  1:177964/1‑146 (MQ=255)                                                                                                        aTCCTCAAGGCGGTAC‑GCTGGGGATCTACATCGACCACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGat                                     <  7:233170/149‑1 (MQ=255)                                                                                                          ccTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGatat                                   <  3:313509/149‑1 (MQ=255)                                                                                                              atggCGGTAC‑GCTGTGGATGTACATCGACAACGTCGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCATCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAAt                               <  7:41648/147‑1 (MQ=255)                                                                                                                 gCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGaa                            <  8:254068/149‑1 (MQ=255)                                                                                                                   ggTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAgg                          >  3:345215/1‑149 (MQ=255)                                                                                                                    gTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAggg                         >  4:201291/1‑149 (MQ=255)                                                                                                                       c‑GCTGTGGATCTACATCGACAACGATGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCtt                      >  7:133692/1‑149 (MQ=255)                                                                                                                           tgtgGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTAt                   >  1:3556/1‑149 (MQ=255)                                                                                                                                    aCATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTc          >  3:675/1‑149 (MQ=255)                                                                                                                                     cATCGACAACGATGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTc          <  8:133692/148‑1 (MQ=255)                                                                                                                                     cATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTc             <  5:267487/145‑1 (MQ=255)                                                                                                                                         gACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATa      <  2:177964/148‑1 (MQ=255)                                                                                                                                         gACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATa      <  3:136070/148‑1 (MQ=255)                                                                                                                                          aCAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATAcc    >  6:248328/1‑149 (MQ=255)                                                                                                                                            aaCGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGa  >  7:167366/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                ATCCAATGGGCACGGCGCTACGACAGCAGGGACATGCGCAGCGACGGTCTACTGGGGATGGGTTGGAGTGTCCCCTATGAAGTGGAGCTGGCCCGCGTCCCACATCCTCAAGGCGGTAC‑GCTGTGGATCTACATCGACAACGACGGTAACCGACTGGAACTGGGCCGCCTCAGTGCCGGTGATGCCTTCATCAGTGCCGTGGACGGCTTGGCCTTCTTCCAGCTGGAGGACGGCCAGACCGTTGTCGAAGATATCAATGAAGGGCTTTATCGGGTCTTCGATACCGA  >  NC_002947/4614578‑4614864

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: ‑