Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	307,836	A→G	7.3%	E28E (GAA→GAG)	lytR →	response regulator LytR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	307,836	0	A	G	7.3%	157.4 / 2.3	54	E28E (GAA→GAG)	lytR	response regulator LytR
Reads supporting (aligned to +/- strand):  ref base A (23/27);  new base G (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

CGGTACCACTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAGATGAAAGAGCC  >  CP000730/307699‑307973                                                                                                                                          |                                                                                                                                          cGGTACCACTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAAtt                                                                                                                                        <  2:333876/141‑1 (MQ=255)    tACCACTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAAt                                                                                                                                     >  1:503366/1‑141 (MQ=255)        aCTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAgg                                                                                                                                 >  1:316914/1‑141 (MQ=255)         cTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGc                                                                                                                                <  1:41965/141‑1 (MQ=255)             ttGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTgaagaa                                                                                                                                           >  2:595266/1‑126 (MQ=255)             ttGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTgaagaa                                                                                                                                           <  1:595266/126‑1 (MQ=255)              tttttttttttttcTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGaaa                                                                                                                           >  2:93919/14‑141 (MQ=255)                gtgtgtACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAAt                                                                                                                         >  1:149207/1‑141 (MQ=255)                         tCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAg                                                                                                                              <  1:647931/127‑1 (MQ=255)                         tCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAg                                                                                                                              >  2:647931/1‑127 (MQ=255)                         tCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGaa                                                                                                                >  2:461969/1‑141 (MQ=255)                                gAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTgg                                                                                                         <  1:636118/141‑1 (MQ=255)                                 aaaGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGa                                                                                                        >  1:192383/1‑141 (MQ=255)                                      cAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCac                                                                                                   <  2:476639/141‑1 (MQ=255)                                       aagaagAGGAATAAATATGAAACCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTTAAAGAAACATTGGAAGCact                                                                                                  <  1:148278/141‑1 (MQ=255)                                       aaGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCact                                                                                                  >  2:70112/1‑141 (MQ=255)                                       aaGAGGAGGAACAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCact                                                                                                  >  2:149086/1‑141 (MQ=255)                                        agagGACGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTGCTGACTTAACCTATTTATCAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCacta                                                                                                 <  1:709471/141‑1 (MQ=255)                                           ggaggaATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTg                                                                                              >  2:317550/1‑141 (MQ=255)                                                  taaataTGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATGAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGatcaatc                                                                                       >  1:544470/1‑141 (MQ=255)                                                     atatGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAGATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATcaatcaat                                                                                    >  2:303821/1‑141 (MQ=255)                                                     atatGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAGATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTCATcaatcaat                                                                                    >  2:303822/1‑141 (MQ=255)                                                     atatGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATcaatcaat                                                                                    >  1:213482/1‑141 (MQ=255)                                                     atatGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATcaatcaat                                                                                    >  2:303801/1‑141 (MQ=255)                                                             gCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACAtt                                                                            <  2:113042/141‑1 (MQ=255)                                                              cATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATta                                                                           >  1:47707/1‑141 (MQ=255)                                                               aTTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATtat                                                                          <  1:503359/141‑1 (MQ=255)                                                                ttAATCATAGATGATGAGCCATTAGCACGTAATGACTTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATtata                                                                         >  2:700565/1‑141 (MQ=255)                                                                   aTCATAGATGATGATCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGAAAGCACTACTGATCAATCAATATGACATTATAttt                                                                      >  2:454458/1‑141 (MQ=255)                                                                   aTCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATAttt                                                                      >  2:112268/1‑141 (MQ=255)                                                                          atgatgGGCGATTAGCACGTATTGAATTAACATATTTATGAAAGGAAATTGGTGGGTTTGAAGAAATTAATGAGCCAGAAAATGCAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATAGTTTTAGATg                                                               <  2:116580/141‑1 (MQ=255)                                                                           tgatgaGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGt                                                              <  1:238042/141‑1 (MQ=255)                                                                           tgatgaGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGt                                                              <  2:546607/141‑1 (MQ=255)                                                                                aGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAAtt                                                         <  1:323103/141‑1 (MQ=255)                                                                                  ccATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTa                                                       <  1:126224/141‑1 (MQ=255)                                                                                      tAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATgg                                                   <  1:386415/141‑1 (MQ=255)                                                                                        gCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGAt                                                 >  1:617851/1‑141 (MQ=255)                                                                                            gTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGaaa                                             <  2:20253/141‑1 (MQ=255)                                                                                              aaTGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAAt                                           >  2:41586/1‑141 (MQ=255)                                                                                                   aTTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGAt                                      >  1:488718/1‑141 (MQ=255)                                                                                                   aTTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACGACTGATGAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGAt                                      >  1:136585/1‑141 (MQ=255)                                                                                                     tAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCg                                    <  1:317550/141‑1 (MQ=255)                                                                                                         atatTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAAtt                                <  1:218689/141‑1 (MQ=255)                                                                                                           atttattAAATGAAATTGGTGGTTTTGAAGAGATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAg                              <  1:303821/141‑1 (MQ=255)                                                                                                           atttattAAATGAAATTGGTGGTTTTGAAGAGATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAg                              <  1:303822/141‑1 (MQ=255)                                                                                                           atttattAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAg                              <  1:303801/141‑1 (MQ=255)                                                                                                               attaAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGc                          <  1:113316/141‑1 (MQ=255)                                                                                                                ttaAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCt                         <  2:209004/141‑1 (MQ=255)                                                                                                                  aaaTGATAATGATGGTATTGAAGAAATTAATGCGTCGGAAAATGTTAAAGCAACATTGGAAGCAATACTGATCAATCAATATGACATTATATTTTTAGAGGTCAATTTAATGGATGAAAATGGGCTCGAATTAGGGGCTaa                       <  2:684104/141‑1 (MQ=255)                                                                                                                    aTGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGa                     <  1:399360/141‑1 (MQ=255)                                                                                                                    aTGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGAGGAAAATGGGATCGAATTAGGAGCTAAGa                     <  1:230472/141‑1 (MQ=255)                                                                                                                     tGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGAt                    <  2:298001/141‑1 (MQ=255)                                                                                                                       aaaTTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAACATGGGATCGAATTAGGAGCCAAGATTc                  >  1:489153/1‑141 (MQ=255)                                                                                                                            ggtggtTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTATATGTCATTTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAg             >  2:47235/1‑141 (MQ=255)                                                                                                                             gtggtTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAGa            <  1:701347/141‑1 (MQ=255)                                                                                                                                gtTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAGATGa         <  2:340758/141‑1 (MQ=255)                                                                                                                                       agaaATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAGATGAAAGAGcc  >  2:143970/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                          CGGTACCACTTTTTGGTGTGTACTTCCTTATGAAAGACAAGAGGAGGAATAAATATGAAAGCATTAATCATAGATGATGAGCCATTAGCACGTAATGAATTAACATATTTATTAAATGAAATTGGTGGTTTTGAAGAAATTAATGAGGCAGAAAATGTAAAAGAAACATTGGAAGCACTACTGATCAATCAATATGACATTATATTTTTAGATGTCAATTTAATGGATGAAAATGGGATCGAATTAGGAGCTAAGATTCAAAAGATGAAAGAGCC  >  CP000730/307699‑307973

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑