Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	459,256	T→C	100%	D123D (GAT→GAC)	lon →	DNA‑binding ATP‑dependent protease La

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	459,256	0	T	C	99.8%	251.1 / ‑7.0	71	D123D (GAT→GAC)	lon	DNA‑binding ATP‑dependent protease La
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (30/40);  minor base A (0/1);  total (30/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTCGAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGATGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGACGT  >  NC_000913/459160‑459350                                                                                                 |                                                                                               ggTCGAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAGTGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATtgacga                                                                                              <  2:1596091/99‑1 (MQ=255) ggTCGAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAg                                                                                             >  2:1755395/1‑100 (MQ=255)    cGAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCgg                                                                                          >  2:1330207/1‑100 (MQ=255)     gAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCggg                                                                                         >  2:1511333/1‑100 (MQ=255)     gAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCggg                                                                                         >  1:71888/1‑100 (MQ=255)     gAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCggg                                                                                         <  1:2489459/100‑1 (MQ=255)     gAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCggg                                                                                         <  1:2364759/100‑1 (MQ=255)     gAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCgcg                                                                                         <  1:1741488/100‑3 (MQ=255)       ggggTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGaa                                                                                       >  1:1401483/1‑100 (MQ=255)         ggTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACa                                                                                     <  2:669205/100‑1 (MQ=255)           ttACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAgg                                                                                   <  1:1305009/100‑1 (MQ=255)           ttACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAgg                                                                                   <  1:738852/100‑1 (MQ=255)             aCAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGaa                                                                                 <  1:2208644/100‑1 (MQ=255)             aCAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGaa                                                                                 >  1:2376873/1‑100 (MQ=255)               aGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAg                                                                                <  2:2374764/99‑1 (MQ=255)               aGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGt                                                                               >  1:218093/1‑100 (MQ=255)                 cgcgcgcgTATTTCTGCGCTCTCGGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCAGTGACGAGCGGGAACAGGAAg                                                                                <  2:2277470/97‑1 (MQ=255)                 cgcgcgcgTAGTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGc                                                                             <  2:241978/100‑1 (MQ=255)                  gcgcgcgTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCt                                                                            <  2:421222/100‑1 (MQ=255)                    gcgcgTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTgg                                                                          >  2:2370219/1‑100 (MQ=255)                    gcgcgTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTgg                                                                          <  2:2551937/100‑1 (MQ=255)                    gcgcgTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTgg                                                                          <  2:2551054/100‑1 (MQ=255)                     cgcgTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACAATTGACGAGCGGGAACAGGAAGTGCTGGt                                                                         >  2:2008790/1‑100 (MQ=255)                           tttCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTAc                                                                   <  1:346072/100‑1 (MQ=255)                             tCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTg                                                                 >  1:289003/1‑100 (MQ=255)                             tCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTg                                                                 >  2:2103695/1‑100 (MQ=255)                              cTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGc                                                                <  2:824191/100‑1 (MQ=255)                                gcgcTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGTCCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCaa                                                              >  2:1454309/1‑100 (MQ=255)                                   ctctctGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCa                                                           >  1:130194/1‑100 (MQ=255)                                     ctctGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGc                                                         >  1:1613769/1‑100 (MQ=255)                                     ctctGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGc                                                         <  2:673656/100‑1 (MQ=255)                                      tctGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGcc                                                        <  2:414864/100‑1 (MQ=255)                                        tGACAATGGCGCACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCGGGTGCGTACTGCAATCAGCCAg                                                      <  2:2112115/100‑1 (MQ=255)                                        tGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAg                                                      >  2:2556079/1‑100 (MQ=255)                                         gACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGt                                                     >  2:120259/1‑100 (MQ=255)                                           cAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTc                                                   <  1:2052258/100‑1 (MQ=255)                                           cAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTc                                                   >  1:1477032/1‑100 (MQ=255)                                             aTGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGa                                                 <  2:288999/100‑1 (MQ=255)                                             aTGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGa                                                 <  2:2326371/100‑1 (MQ=255)                                              tGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGaa                                                <  1:2265989/100‑1 (MQ=255)                                               ggCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAg                                               >  2:823525/1‑100 (MQ=255)                                               ggCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAg                                               <  2:2292823/100‑1 (MQ=255)                                               ggCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAg                                               <  1:2556027/100‑1 (MQ=255)                                               ggCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAg                                               <  1:2556095/100‑1 (MQ=255)                                                  gAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCt                                            <  1:676670/100‑1 (MQ=255)                                                       cTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGTCAGTTCGAAGGCTACATc                                       >  1:691140/1‑100 (MQ=255)                                                       cTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATc                                       <  1:1332980/100‑1 (MQ=255)                                                       cTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATc                                       >  1:48461/1‑100 (MQ=255)                                                            cTGCGAAGGCGGAGTATCTGGAGTCGCCGACCCTTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCt                                  >  2:846879/1‑100 (MQ=255)                                                              gCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGCAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGc                                   >  2:598460/1‑97 (MQ=255)                                                              gCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGa                                <  2:325651/100‑1 (MQ=255)                                                               cGAAGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGaa                               <  2:491359/100‑1 (MQ=255)                                                                  aGGCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATTAAGCTGAACa                             <  1:645810/99‑1 (MQ=255)                                                                   ggCGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACaaa                           <  1:647384/100‑1 (MQ=255)                                                                     cGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACaaaaa                         <  2:1613758/100‑1 (MQ=255)                                                                     cGGAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACaaaaa                         >  2:1304445/1‑100 (MQ=255)                                                                      ggAGTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACaaaaaa                        >  1:915734/1‑100 (MQ=255)                                                                         gTATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATc                     <  1:1244147/100‑1 (MQ=255)                                                                          tATCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATcc                    <  1:967374/100‑1 (MQ=255)                                                                           aTCTGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATccc                   <  1:1233614/100‑1 (MQ=255)                                                                              tGGAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCccacc                <  1:1511344/100‑1 (MQ=255)                                                                                gAGTCGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAATAAAATCccacctg              <  1:1727300/100‑3 (MQ=255)                                                                                    cGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGt          >  1:2239686/1‑100 (MQ=255)                                                                                    cGCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGt          >  2:779045/1‑100 (MQ=255)                                                                                     gCCGACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTg         >  1:759873/1‑100 (MQ=255)                                                                                       cGACCATTGAAGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCGAGTTCGAAGGCTACATAAAGCTGAACAAAAAAATCCCACCAGAAGTGCt       <  2:1789540/100‑1 (MQ=255)                                                                                        gACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTg      <  1:94624/100‑1 (MQ=255)                                                                                        gACCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTg      <  1:1895710/100‑1 (MQ=255)                                                                                         aCCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGa     >  2:1944897/1‑100 (MQ=255)                                                                                         aCCATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGa     <  2:900468/100‑1 (MQ=255)                                                                                          ccATTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGAc    >  2:1992693/1‑100 (MQ=255)                                                                                            aTTGACGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGACGt  >  2:2413429/1‑100 (MQ=255)                                                                                                 |                                                                                               GGTCGAGGGGTTACAGCGCGCGCGTATTTCTGCGCTCTCTGACAATGGCGAACACTTTTCTGCGAAGGCGGAGTATCTGGAGTCGCCGACCATTGATGAGCGGGAACAGGAAGTGCTGGTGCGTACTGCAATCAGCCAGTTCGAAGGCTACATCAAGCTGAACAAAAAAATCCCACCAGAAGTGCTGACGT  >  NC_000913/459160‑459350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑