Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,880,549	T→C	100%	T71A (ACC→GCC)	leuE ←	leucine efflux protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,880,549	0	T	C	98.6%	230.1 / ‑4.5	69	T71A (ACC→GCC)	leuE	leucine efflux protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (26/41);  total (26/43)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

TTTACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATA  >  NC_000913/1880454‑1880643                                                                                                |                                                                                               tttACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCtta                                                                                            <  2:976604/100‑1 (MQ=255)   tACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaat                                                                                          <  1:343507/100‑1 (MQ=255)   tACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaat                                                                                          <  2:675029/100‑1 (MQ=255)   ctcccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaat                                                                                          <  2:686260/98‑1 (MQ=255)     cccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaatag                                                                                        >  1:686267/1‑98 (MQ=255)      ccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaattaa                                                                                       <  1:2438002/100‑1 (MQ=255)      ccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaattaa                                                                                       >  1:1863647/1‑100 (MQ=255)       cTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTtaattaat                                                                                      <  2:266981/100‑1 (MQ=255)       cTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTtaattaat                                                                                      <  1:2006458/100‑1 (MQ=255)            gggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGc                                                                                 <  2:778987/100‑1 (MQ=255)            gggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGc                                                                                 >  1:390168/1‑100 (MQ=255)            gggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGc                                                                                 <  2:2183474/100‑1 (MQ=255)              gTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCa                                                                               >  1:666340/1‑100 (MQ=255)                cgcgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACt                                                                             <  2:531255/100‑1 (MQ=255)                 gcgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTc                                                                            <  1:1695721/100‑1 (MQ=255)                   gTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCa                                                                          >  1:580474/1‑100 (MQ=255)                   gTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCa                                                                          <  2:2351917/100‑1 (MQ=255)                    tAAAGAATTTTACT‑CCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                        <  2:2540027/100‑1 (MQ=255)                      aaGAATTTTACTCCCCAGATAGAGCCAATAAAACGCACCAAGATAACTTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGcc                                                                       <  2:2181886/100‑1 (MQ=255)                       aGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGccc                                                                      <  1:1015730/100‑1 (MQ=255)                          aTTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATg                                                                   <  1:155738/100‑1 (MQ=255)                           ttttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATATCGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGc                                                                  <  2:1716916/100‑1 (MQ=255)                           ttttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGc                                                                  <  1:2128073/100‑1 (MQ=255)                            tttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGcc                                                                 <  1:1353539/100‑1 (MQ=255)                            tttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGcc                                                                 <  1:1790759/100‑1 (MQ=255)                             ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                                >  2:1357456/1‑100 (MQ=255)                             ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                                <  2:471304/100‑1 (MQ=255)                                  ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTCATGTCGCCACTCCAGCCCATGCCAGAAAc                                                           >  2:2496851/1‑100 (MQ=255)                                  ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                           >  1:1400115/1‑100 (MQ=255)                                    ccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                             <  2:1075494/96‑1 (MQ=255)                                     cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                        <  2:2476194/100‑1 (MQ=255)                                     cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                        <  1:1616732/100‑1 (MQ=255)                                        aTAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCCCTCCAGCCCATGCCAGAAACATCAAt                                                     <  1:2247835/100‑1 (MQ=255)                                         tAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATa                                                    <  1:285945/100‑1 (MQ=255)                                           gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATAcc                                                  >  2:1440180/1‑100 (MQ=255)                                           gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATAcc                                                  >  2:43114/1‑100 (MQ=255)                                           gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCACCACCCCAGCCTATGCCAGAAACATCaa                                                      >  2:796195/1‑96 (MQ=255)                                            agCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCg                                                 >  1:460608/1‑100 (MQ=255)                                              cAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCa                                               <  2:837919/100‑1 (MQ=255)                                                  tAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGc                                           <  2:2006802/100‑1 (MQ=255)                                                   aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                          <  2:390164/100‑1 (MQ=255)                                                    aaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                         >  1:318373/1‑100 (MQ=255)                                                     aaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaa                                        >  1:1848967/1‑100 (MQ=255)                                                       cgcgCCAGGATACCGAAAAATGTTGAATAAGACCGGGCTCGACTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaat                                       <  2:2240056/99‑1 (MQ=255)                                                        gCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataa                                     <  1:2326074/100‑1 (MQ=255)                                                         cACCAAGATAACGTACAATGTTGAATTATATCGGGGTGGCCTTAATTAATGTAGCCACTACAGCCCATGCCAGAAACATCAATAACGCATCGCCaataca                                    >  2:1542475/1‑98 (MQ=255)                                                         cACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaa                                    >  1:260532/1‑100 (MQ=255)                                                         cACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCAGGCCAGAAACATCAATACCGCATCGCCaataaa                                    >  1:2559639/1‑100 (MQ=255)                                                          aCCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaat                                   <  2:2401157/100‑1 (MQ=255)                                                                 tAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGc                            <  2:1630099/100‑1 (MQ=255)                                                                      tACAATGTTGAATAATATCGGGGTGGCCATAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGcc                       >  1:314576/1‑100 (MQ=255)                                                                       aCAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCg                      <  2:2338995/100‑1 (MQ=255)                                                                       aCAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCg                      >  2:898599/1‑100 (MQ=255)                                                                          aTGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCaa                   <  1:1183162/100‑1 (MQ=255)                                                                          aTGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCaa                   >  2:1142264/1‑100 (MQ=255)                                                                           tGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAg                  <  2:580467/100‑1 (MQ=255)                                                                             ttGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAGTACACCGCAGGCCGCAAGAt                <  2:1569636/100‑1 (MQ=255)                                                                              tGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATa               <  2:1244413/100‑1 (MQ=255)                                                                                aataatATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAc             >  1:1381532/1‑100 (MQ=255)                                                                                 ataataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAcc            >  2:1858541/1‑100 (MQ=255)                                                                                 ataataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAcc            <  1:2496779/100‑1 (MQ=255)                                                                                 ataataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAcc            >  1:2268266/1‑100 (MQ=255)                                                                                   aataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGc          >  1:2507009/1‑100 (MQ=255)                                                                                     tatCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCt        <  1:668280/100‑1 (MQ=255)                                                                                       tCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCttt      <  1:41628/100‑1 (MQ=255)                                                                                       tCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCACATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCttt      <  1:1430241/100‑1 (MQ=255)                                                                                        cGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTc     <  2:2442443/100‑1 (MQ=255)                                                                                         ggggTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCa    >  2:2363782/1‑100 (MQ=255)                                                                                          gggTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCAt   >  2:55199/1‑100 (MQ=255)                                                                                           ggtggcCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATa  <  2:1673157/100‑1 (MQ=255)                                                                                                |                                                                                               TTTACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATA  >  NC_000913/1880454‑1880643

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: ‑