Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,340,287	G→A	L79F (CTT→TTT)	adiA ←	arginine decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,340,287	0	G	A	91.8%	203.0 / 8.5	74	L79F (CTT→TTT)	adiA	arginine decarboxylase
Reads supporting (aligned to +/- strand):  ref base G (2/4);  new base A (31/36);  total (33/41)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01

TCATCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAGAAT  >  NC_000913/4340190‑4340383                                                                                                  |                                                                                                 tCATCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACt                                                                                                <  2:490253/100‑1 (MQ=255)  cATCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACtt                                                                                               >  1:257746/1‑100 (MQ=255)      gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                           <  1:1033974/100‑1 (MQ=255)      gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                           <  1:1553576/100‑1 (MQ=255)       aCAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGa                                                                                          <  1:812559/100‑1 (MQ=255)        cAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGAt                                                                                         >  1:350230/1‑100 (MQ=255)            cTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAAt                                                                                     <  2:229405/100‑1 (MQ=255)              ccAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTg                                                                                   >  2:651958/1‑100 (MQ=255)              ccAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTg                                                                                   >  2:457414/1‑100 (MQ=255)                agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                                 <  2:1808845/100‑1 (MQ=255)                  cagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTg                                                                               <  1:1029673/100‑1 (MQ=255)                     gTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACg                                                                            >  2:1878521/1‑100 (MQ=255)                        ncgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                         >  2:849234/2‑100 (MQ=255)                        gcgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                         >  1:1304749/1‑100 (MQ=255)                        gcgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                         >  2:230527/1‑100 (MQ=255)                        gcgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                         >  1:1304742/1‑100 (MQ=255)                          gATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCCATTGTCTGACGTTTTg                                                                       >  1:815596/1‑100 (MQ=255)                          gATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTg                                                                       >  1:1128714/1‑100 (MQ=255)                             ccATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATg                                                                    >  1:506352/1‑100 (MQ=255)                             ccATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATg                                                                    >  2:1529756/1‑100 (MQ=255)                                ttGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTc                                                                 <  1:1838707/100‑1 (MQ=255)                                 tGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCg                                                                <  1:1881582/100‑1 (MQ=255)                                 tGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCg                                                                <  1:946517/100‑1 (MQ=255)                                    ggcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTcc                                                             >  2:1069148/1‑100 (MQ=255)                                    ggcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTcc                                                             <  1:31453/100‑1 (MQ=255)                                       gAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGa                                                          <  2:1229173/100‑1 (MQ=255)                                         gggCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATg                                                        <  2:1568159/100‑1 (MQ=255)                                           gCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGtt                                                      >  2:1577343/1‑100 (MQ=255)                                            cTTTTTCCCGGTCGCCCAACAGGATGACCGGCACGTTTTGTTGGCGCTCATGAATCTTACCGATCAATTGTCTGACTTTTTGATGTTCGTCCGGa                                                          <  1:1648701/95‑1 (MQ=255)                                             tttttCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTcc                                                    <  1:1304663/100‑1 (MQ=255)                                              ttttCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTcc                                                    <  1:1556909/99‑1 (MQ=255)                                              ttttCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCa                                                   >  1:703423/1‑100 (MQ=255)                                                 tCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCAttt                                                <  1:1284315/100‑1 (MQ=255)                                                  cccGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTg                                               >  2:798117/1‑100 (MQ=255)                                                  atctaTCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTg                                               <  1:33520/96‑1 (MQ=255)                                                    cGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGAt                                             >  2:1540278/1‑100 (MQ=255)                                                    cGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGAt                                             >  2:790727/1‑100 (MQ=255)                                                     gATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATa                                            >  1:1659/1‑100 (MQ=255)                                                      aTCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGagat                                           >  2:33520/1‑97 (MQ=255)                                                       tCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGc                                          <  1:457412/100‑1 (MQ=255)                                                        cGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCt                                         >  2:591894/1‑100 (MQ=255)                                                         gCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTg                                        <  1:1854802/100‑1 (MQ=255)                                                          cccAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGa                                       >  1:317842/1‑100 (MQ=255)                                                           ccAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCCATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGaa                                      >  1:1715801/1‑100 (MQ=255)                                                           ccAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGaa                                      <  1:258900/100‑1 (MQ=255)                                                            cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                     <  1:1304073/100‑1 (MQ=255)                                                             aaCAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACa                                    <  1:384114/100‑1 (MQ=255)                                                               cAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATc                                  <  1:329594/100‑1 (MQ=255)                                                                 ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                                <  2:1601822/100‑1 (MQ=255)                                                                  gAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAgg                               <  1:468948/100‑1 (MQ=255)                                                                   aaGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACGGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGc                              >  1:1047891/1‑100 (MQ=255)                                                                       ccGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTc                          >  1:1595930/1‑100 (MQ=255)                                                                        cGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCa                         >  2:100845/1‑100 (MQ=255)                                                                           cACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATg                      <  2:1368658/100‑1 (MQ=255)                                                                           cACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATg                      <  2:703424/100‑1 (MQ=255)                                                                           cACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATg                      <  2:963818/100‑1 (MQ=255)                                                                             cGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGc                    >  2:236160/1‑100 (MQ=255)                                                                             cGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGc                    <  2:1405624/100‑1 (MQ=255)                                                                             cGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGc                    <  2:1391177/100‑1 (MQ=255)                                                                                   gttgGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtt              <  1:1577332/100‑1 (MQ=255)                                                                                   gttgGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtt              <  1:1878509/100‑1 (MQ=255)                                                                                   gttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtt              <  2:749639/100‑1 (MQ=255)                                                                                    ttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGttt             <  2:317844/100‑1 (MQ=255)                                                                                    ttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGttt             <  1:801153/100‑1 (MQ=255)                                                                                      ggCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtttca           >  1:1717169/1‑98 (MQ=255)                                                                                      ggCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGa           >  1:1420135/1‑100 (MQ=255)                                                                                       gcgcTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTGCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGaa          <  1:653961/100‑1 (MQ=255)                                                                                        cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAag         <  1:467050/100‑1 (MQ=255)                                                                                        cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAag         <  1:868968/100‑1 (MQ=255)                                                                                        cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAag         <  2:565690/100‑1 (MQ=255)                                                                                            cATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagagag     <  1:1090376/100‑1 (MQ=255)                                                                                            cATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagagag     >  2:261293/1‑100 (MQ=255)                                                                                             aTGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAgagaga    >  2:1178988/1‑100 (MQ=255)                                                                                               gAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAGAAt  >  1:1857140/1‑100 (MQ=255)                                                                                                  |                                                                                                 TCATCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAGAAT  >  NC_000913/4340190‑4340383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑