Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	77,758:1	+C	10.0%	coding (138/1179 nt)	setA →	broad specificity sugar efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	77,758	1	.	C	10.0%	150.4 / 14.9	40	coding (138/1179 nt)	setA	broad specificity sugar efflux system
Reads supporting (aligned to +/- strand):  ref base . (17/19);  new base C (2/2);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.49e-01

GGGAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATGGCTATCGGCAAT  >  NC_000913/77613‑77899                                                                                                                                                   |                                                                                                                                              gggAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑Caa                                                                                                                                            >  3:230669/1‑149 (MQ=255)        tATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCt                                                                                                                                     <  4:201804/149‑1 (MQ=255)            aTCTGGATAATGTCGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGAt                                                                                                                                 <  3:123111/149‑1 (MQ=255)            aTCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGAt                                                                                                                                 >  1:445481/1‑149 (MQ=255)                    aaTGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCctca                                                                                                                         >  4:306409/1‑148 (MQ=255)                     aTGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCtt                                                                                                                        <  4:230669/149‑1 (MQ=255)                       gACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCtttt                                                                                                                      >  1:430574/1‑149 (MQ=255)                       gACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCtttt                                                                                                                      <  4:146010/149‑1 (MQ=255)                          gATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTtata                                                                                                                   <  4:221275/149‑1 (MQ=255)                                  gCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCt                                                                                                                                     >  1:420179/1‑123 (MQ=255)                                  gCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCt                                                                                                                                     <  2:420179/123‑1 (MQ=255)                                                       cgGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTa                                                                                      >  2:279965/1‑149 (MQ=255)                                                        ggCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTaa                                                                                     <  2:430574/149‑1 (MQ=255)                                                          cATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGc                                                                                   <  1:227976/149‑1 (MQ=255)                                                              tATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCctct                                                                               <  3:32146/149‑1 (MQ=255)                                                                   tGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTg                                                                          >  3:159219/1‑149 (MQ=255)                                                                     gTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGc                                                                        >  2:234507/1‑149 (MQ=255)                                                                          ttttATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAAc                                                                   <  2:445481/149‑1 (MQ=255)                                                                          ttttATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAAc                                                                   >  1:202564/1‑149 (MQ=255)                                                                          ttttATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAAc                                                                   >  1:252080/1‑149 (MQ=255)                                                                              atgatgGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGTAAAACGTTc                                                               <  4:279153/149‑1 (MQ=255)                                                                                   gggggTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACa                                                          <  4:281759/149‑1 (MQ=255)                                                                                            cGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCg                                                 >  3:76549/1‑149 (MQ=255)                                                                                             ggggCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGa                                                <  1:234507/149‑1 (MQ=255)                                                                                                           tCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGa                                  >  1:441598/1‑149 (MQ=255)                                                                                                              tACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATta                               >  4:206518/1‑149 (MQ=255)                                                                                                                    gAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATAtttt                         <  3:206518/149‑1 (MQ=255)                                                                                                                        ttATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTc                                                               >  3:22856/1‑107 (MQ=255)                                                                                                                        ttATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTc                                                               <  4:22856/107‑1 (MQ=255)                                                                                                                          aTTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACTGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGtt                   <  3:306409/149‑1 (MQ=255)                                                                                                                               tGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATg              <  4:76549/149‑1 (MQ=255)                                                                                                                                    agaaaGGTT‑GCGCGCCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATg              <  3:347566/140‑1 (MQ=255)                                                                                                                                    agaaaGGTT‑GCGCGCCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATg              >  4:347566/5‑144 (MQ=255)                                                                                                                                     gaaaGGTT‑GCGCGCCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATg              >  4:119695/4‑143 (MQ=255)                                                                                                                                     gaaaGGTT‑GCGCGCCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATg              <  3:119695/140‑1 (MQ=255)                                                                                                                                     gTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGAt               >  1:440147/1‑142 (MQ=255)                                                                                                                                     gTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGAt               <  2:440147/142‑1 (MQ=255)                                                                                                                                          gTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATGGCTATCGGCaa   <  4:159219/149‑1 (MQ=255)                                                                                                                                           ttGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATGGCTATCGGCAAt  >  4:219071/1‑149 (MQ=255)                                                                                                                                           ttGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATGGCTATCGGCAAt  >  3:316378/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                              GGGAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCG‑CAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATGGCTATCGGCAAT  >  NC_000913/77613‑77899

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑