Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,880,549	T→C	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	98.2%	186.5 / ‑6.0	55	T71A (ACC→GCC)	leuE	leucine efflux protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (26/28);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTC  >  NC_000913/1880458‑1880640                                                                                            |                                                                                            cccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaatta                                                                                     >  1:788118/1‑100 (MQ=255)   cTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTtaattaat                                                                                   >  1:653735/1‑100 (MQ=255)      cAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATg                                                                                  >  2:1568520/1‑98 (MQ=255)         ggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGcc                                                                             <  1:1082589/100‑1 (MQ=255)            cgcgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACt                                                                          >  1:1321114/1‑100 (MQ=255)              cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATATCACGACTcc                                                                        >  2:463220/1‑100 (MQ=255)                tAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAg                                                                      <  1:1373197/100‑1 (MQ=255)                tAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAg                                                                      >  1:240213/1‑100 (MQ=255)                 aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAga                                                                     >  2:1373190/1‑99 (MQ=255)                 aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                     >  1:489569/1‑100 (MQ=255)                      aTTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATg                                                                >  2:983501/1‑100 (MQ=255)                      aTTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATg                                                                <  1:903135/100‑1 (MQ=255)                        tttACTCCCCAGATAGAGCAAATAAAACGCAGCAAGATCACATACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGc                                                               <  2:1108086/99‑1 (MQ=255)                         ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                             <  1:1132005/100‑1 (MQ=255)                           ccgatctaGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGa                                                           <  1:441834/93‑1 (MQ=255)                            cTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          >  2:1130848/1‑100 (MQ=255)                            cTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTCATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          >  2:1516547/1‑100 (MQ=255)                             tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         <  2:511019/100‑1 (MQ=255)                             tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         >  2:1241740/1‑100 (MQ=255)                             tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          <  2:1299496/99‑1 (MQ=255)                             tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTAGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         >  2:1201227/1‑100 (MQ=255)                              ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        >  1:459215/1‑100 (MQ=255)                              ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        <  1:501100/100‑1 (MQ=255)                              ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        <  2:1324789/100‑1 (MQ=255)                              ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCAATGCCAGAAAc                                                        <  2:1408479/100‑1 (MQ=255)                                 cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                     <  2:467538/100‑1 (MQ=255)                                  aGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaagatcgg                                                    >  2:441833/1‑94 (MQ=255)                                  aGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                     <  2:873931/99‑1 (MQ=255)                                   gATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCaa                                                   >  1:873060/1‑100 (MQ=255)                                     tAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATa                                                 >  1:1005735/1‑100 (MQ=255)                                         gCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGc                                             >  2:893249/1‑100 (MQ=255)                                          cAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCa                                            >  1:538679/1‑100 (MQ=255)                                            aaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATc                                          >  1:1368048/1‑100 (MQ=255)                                               aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                       <  1:1516556/100‑1 (MQ=255)                                               aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                       <  1:84464/100‑1 (MQ=255)                                                aaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                      >  1:510182/1‑100 (MQ=255)                                                aaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                      >  1:855297/1‑100 (MQ=255)                                                   cGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaata                                   <  2:700442/100‑1 (MQ=255)                                                   cGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCAATCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaat                                    >  1:389274/1‑99 (MQ=255)                                                   cGCACCAAGATAACGTACAATGTTGAATAATATCAGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaata                                   <  2:1290352/100‑1 (MQ=255)                                                      aCCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaat                                <  2:485369/100‑1 (MQ=255)                                                         aaGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATaca                             <  2:378397/100‑1 (MQ=255)                                                             tAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGc                         <  1:2998/100‑1 (MQ=255)                                                              aaCGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCGATAAATACACCGCa                        <  2:811324/100‑1 (MQ=255)                                                                 gTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGc                     >  1:604726/1‑100 (MQ=255)                                                                  tACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGcc                    >  1:1374612/1‑100 (MQ=255)                                                                     aaTGTTGAATAATATCGGGGTGGCCTTAATTAAAGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCa                 <  2:51688/100‑1 (MQ=255)                                                                          tGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATa            >  2:163040/1‑100 (MQ=255)                                                                          tGAATAAGATCGGGGTGGCCTTAATTAATGTCGATCCTCCAGCCCATGCCAGAAACAACAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAg               <  2:273543/97‑1 (MQ=255)                                                                            aataatATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAc          >  2:1097273/1‑100 (MQ=255)                                                                             ataataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAcc         <  2:1360843/100‑1 (MQ=255)                                                                              taataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCg        <  1:1241745/100‑1 (MQ=255)                                                                               aataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGc       <  2:788113/100‑1 (MQ=255)                                                                                  atCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCtt    <  1:91472/100‑1 (MQ=255)                                                                                    cGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTc  <  1:1436338/100‑1 (MQ=255)                                                                                            |                                                                                            CCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTC  >  NC_000913/1880458‑1880640

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: ‑