Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,721,390	T→A	8.3%	intergenic (‑352/‑90)	PP_2381 ← / → PP_2382	hypothetical protein/putative transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,721,390	0	T	A	8.3%	130.0 / 3.5	48	intergenic (‑352/‑90)	PP_2381/PP_2382	hypothetical protein/putative transporter
Reads supporting (aligned to +/- strand):  ref base T (17/27);  new base A (2/2);  total (19/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.32e-01

GGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTTCGCTGTCGCTGGGCTACAGCTT  >  NC_002947/2721244‑2721535                                                                                                                                                   |                                                                                                                                                  gggAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAatat                                                                                                                                                 >  3:69806/1‑149 (MQ=255) gggAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAatat                                                                                                                                                 >  1:66093/1‑149 (MQ=255) gggAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAata                                                                                                                                                  <  6:171531/148‑1 (MQ=255)    aaaaTGCCGTCGTGTCTGCATTCATAGAATGGTTGTTGTAGGAAATTTCCTGGTTTCTGATTTTCGCTTGCAGAAAGCTTCGGAGTTGTTTTAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTg                                                                                                                                              <  1:111658/149‑1 (MQ=255)       aTGCCGTCGTGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTTCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCa                                                                                                                                           <  1:272771/149‑1 (MQ=255)          ccGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAAtc                                                                                                                                        <  1:169429/149‑1 (MQ=255)               gggTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAAt                                                                                                                                   <  8:44521/149‑1 (MQ=255)                  tCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGATTGCCAAATATTGGCCAACTCAATcta                                                                                                                                <  3:247763/149‑3 (MQ=38)                      cATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTc                                                                                                                             <  4:69806/148‑1 (MQ=255)                      cATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGATTGCCAAATATTGGCCAACTCAATctaa                                                                                                                               <  2:65083/146‑4 (MQ=38)                       aTTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCa                                                                                                                            >  4:136959/1‑148 (MQ=255)                           aaaGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGa                                                                                                                       <  3:311908/149‑1 (MQ=255)                             aGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGt                                                                                                                     <  5:138419/149‑1 (MQ=255)                             aGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGt                                                                                                                     <  7:139996/149‑1 (MQ=255)                                  ggTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCa                                                                                                                >  4:382184/1‑149 (MQ=255)                                         gtAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGaa                                                                                                          <  6:415647/148‑1 (MQ=255)                                          tAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATc                                                                                                        >  4:26978/1‑149 (MQ=255)                                            ggAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAAtag                                                                                                                                 >  1:265023/1‑120 (MQ=255)                                            ggAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCg                                                                                                                                 <  2:265023/122‑1 (MQ=255)                                            ggAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCt                                                                                                       >  7:380032/1‑148 (MQ=255)                                            ggAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCt                                                                                                       <  6:121081/148‑1 (MQ=255)                                             gAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTg                                                                                                      >  5:178517/1‑148 (MQ=255)                                               aaaTTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCGCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCaa                                                                                                   <  2:328877/149‑1 (MQ=255)                                                  ttCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATc                                                                                                 >  8:132589/1‑148 (MQ=255)                                                     cGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCaa                                                                                              <  3:136959/148‑1 (MQ=255)                                                            cTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGccc                                                                                                                 <  1:181558/122‑1 (MQ=255)                                                            cTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGccc                                                                                                                 >  2:181558/1‑122 (MQ=255)                                                             tGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAg                                                                                      >  7:67048/1‑148 (MQ=255)                                                               aTTTTCGCTTGCAGATAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATGCTTGCCGAGTCTTAGATTGAGTTGGCCATTATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGa                                                                                    <  5:411482/148‑1 (MQ=255)                                                               aTTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAg                                                                                      <  8:237735/146‑1 (MQ=255)                                                                    cGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGAt                                                                               <  8:67048/148‑1 (MQ=255)                                                                       ttGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCg                                                                           >  4:146754/1‑149 (MQ=255)                                                                              aaGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGaa                                                                    <  5:216460/149‑1 (MQ=255)                                                                                     ggCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTAccc                                                              <  1:305766/148‑1 (MQ=255)                                                                                      gCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGc                                                            <  3:26978/149‑1 (MQ=255)                                                                                        gttgttACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTa                                                          <  7:132589/149‑1 (MQ=255)                                                                                               cAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGa                                                   <  8:380032/149‑1 (MQ=255)                                                                                                aaCTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCAATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGa                                                   >  7:225300/1‑148 (MQ=255)                                                                                                   tttCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACAtt                                               >  1:406643/1‑149 (MQ=255)                                                                                                   tttCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACAtt                                               >  4:161551/1‑149 (MQ=255)                                                                                                    ttCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGcc                                                                         >  7:330040/1‑122 (MQ=255)                                                                                                    ttCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGcc                                                                         <  8:330040/122‑1 (MQ=255)                                                                                                     tCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTg                                              <  7:46413/148‑1 (MQ=255)                                                                                                       aTGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTgcg                                            <  3:382184/148‑1 (MQ=255)                                                                                                       aTGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTgcg                                            <  2:66093/148‑1 (MQ=255)                                                                                                                                 ttAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGTGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTtcgctgtc                 >  2:105479/1‑149 (MQ=255)                                                                                                                                    gATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTtcgctgtcgct              >  5:132300/1‑149 (MQ=255)                                                                                                                                    gATTGAGATTGCCAAATATTGGCCAACTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTtcgctgtcgct              >  2:218972/1‑149 (MQ=255)                                                                                                                                     aTTGAGATTGCCAAATATTGGCCAACTCAATCGGCTCAATGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTtcgctgtcgctg             >  4:75567/1‑149 (MQ=255)                                                                                                                                         aGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTTCGCTGTCGCTGGGc          <  6:178517/148‑1 (MQ=255)                                                                                                                                                cAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTTCGCTGTCGCTGGGCTACAGCtt  >  1:7149/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                  GGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGGTTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGAGCGATGTCGCCAGGAAGTACCCGCTAATGCTGACATTGCGCATTAACCCCGGAACGCGTTCGCTGTCGCTGGGCTACAGCTT  >  NC_002947/2721244‑2721535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑