Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,009	T→C	11.1%	D92D (GAT→GAC)	thrC →	threonine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,009	0	T	C	11.1%	79.1 / 2.4	37	D92D (GAT→GAC)	thrC	threonine synthase
Reads supporting (aligned to +/- strand):  ref base T (18/14);  new base C (2/2);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.12e-01

GAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAG  >  NC_000913/3874‑4148                                                                                                                                        |                                                                                                                                            gAAGGTGGATTTTGTCAGCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAACTCCCACAGGAACTCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGtt                                                                                                                                      <  2:202353/143‑1 (MQ=255)            ttttcgcccGCAGTGGCAAGATCCTCTCGGCGTTTATGGGGGATGAAATCCCACAGGAAAGCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTg                                                                                                                           <  2:410087/137‑1 (MQ=255)              gTCACCCGCAGTGCGAAGATCCTCTCGGAGTTTATTGGTGATGAAATCCTACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGtt                                                                                                                         >  1:179854/1‑143 (MQ=255)                   ccGGAGTGCGGAGGTCCTGTCGGCGGTTATTGGGGATGGAATCCCACAGGAAATCCTGGAAGCGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACg                                                                                                                    <  2:197411/143‑1 (MQ=255)                           cGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAGTGTTGAAAGCGATGTCGGTTGTCTGGAACGGTTCCACGGGCCAACg                                                                                                            >  2:335550/1‑143 (MQ=255)                            gAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCATTCCCGGCTCCGGTCGCCCATGTTGAAAGACATGTCGGGTGTATGGAATTCTTCCACGGCCCAACGc                                                                                                           >  2:494207/1‑143 (MQ=255)                                     ctcGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTACGCGCGGCGTTTGCCTTCCCGGCGCCGGGCGCCAATGTTGAAANCGAGGTCGGCAGTCTGGCATTGTTCCACGCGCCACCCCTGGCCTTTa                                                                                                  >  2:55784/1‑143 (MQ=255)                                       cGGCGTTTATTGGTGATGAAATCCCACAGGAACGCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTaaa                                                                                                <  2:151759/143‑1 (MQ=255)                                        ggCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAg                                                                                               >  1:157755/1‑143 (MQ=255)                                         gCGTTTATTGGTGATGATATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGa                                                                                              <  1:5665/143‑1 (MQ=255)                                          tgTTTATCAGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCGTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGAt                                                                                             <  1:163865/142‑1 (MQ=255)                                                  ggTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGACGCCAATGTTGCAACCGATGTCGGACGTCTGGAATCGCTCCACGGGCCAACGCTGGCATTTAAAGATTCcggcgg                                                                                     >  2:153736/1‑143 (MQ=255)                                                    tgatgaAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTTTTCCGCGGGCCAACGCGGGCATTTAAATGTTTCCGCGGTc                                                                                   >  1:43889/1‑143 (MQ=255)                                                    tgatgaAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTc                                                                                   >  1:499980/1‑143 (MQ=255)                                                       tgaAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCGCTGTTGAAAGCGATGTCGGTGGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGAGTTCGGCGGgcgcc                                                                                >  2:321081/1‑142 (MQ=255)                                                        ggaaTCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCtt                                                                               <  1:135456/141‑1 (MQ=255)                                                          aaTCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGACGTCGGTTGTCTGGAATTGTTCCACGGGCCAAc                                                                                                             <  2:91977/111‑1 (MQ=255)                                                          aaTCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGACGTCGGTTGTCTGGAATTGTTCCACGGGCCAAc                                                                                                             >  1:91977/1‑111 (MQ=255)                                                          aaTCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGACGTCGGTTGTCTGGAATTGTTCCACGGGCCAAc                                                                                                             >  1:91879/1‑111 (MQ=255)                                                          aaTCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGACGTCGGTTGTCTGGAATTGTTCCACGGGCCAAc                                                                                                             <  2:91879/111‑1 (MQ=255)                                                                      aaTCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGc                                                                 <  1:565911/143‑1 (MQ=255)                                                                               agggcgcGTGCGCGCGGCGTTGGCGCTCCCGGCTCCGGTCGCCAATGTTGAAGGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCata                                                        <  2:349649/140‑1 (MQ=255)                                                                                         ggcccggcgCTTCTCTTCTCGGCTATGGCCGCCAATGTAGTCAGCGATGTCCGTTTTCTGGTATTGTTCCACGGCCCAACGCTTGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGa                                              <  2:506268/139‑1 (MQ=255)                                                                                          gcgcgGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGTTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGAt                                             >  1:404740/1‑143 (MQ=255)                                                                                                        ttCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTTGCTTTAAGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCAt                               >  1:129254/1‑143 (MQ=255)                                                                                                        ttCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATCGCGGCTGATCAGCCAGCGACCag                               >  2:373164/1‑142 (MQ=255)                                                                                                            cGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGCATCGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTCACCCATCCGGCGGGCGACAAGCCAGTGACCCTTCtc                           >  2:555865/1‑142 (MQ=255)                                                                                                               cTCCCGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGAcc                        <  2:157755/143‑1 (MQ=255)                                                                                                                   ggTCGCCAATGTTGAAAGCGATGTCGGATGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGGTGAACCACAATGGAGGTGATAAGCCAGTAACCAATCTGACCGCGa                    >  2:551440/1‑143 (MQ=255)                                                                                                                          gaTGTGGAGAGGGATGTCGGTTGTCTGGTATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGAAAAGCCAGTGACCATTCTGACCGCGACCTCCgg             <  2:297646/142‑1 (MQ=255)                                                                                                                          aaTGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATAGTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCgg             <  2:499980/143‑1 (MQ=255)                                                                                                                           aTGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTACAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATCGCGGGTGATAAGCCAGTGCCCCCTCTGACCGCGACCTCCCGt            >  2:483189/1‑143 (MQ=255)                                                                                                                           aTGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATCTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGt            >  2:257738/1‑143 (MQ=255)                                                                                                                               tGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATa        >  2:226790/1‑143 (MQ=255)                                                                                                                                 aaaGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATAcc      >  1:459580/1‑143 (MQ=255)                                                                                                                                  aaGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATCTTGCGGGTGATAAGCCAGTGACCACTCTGACCGCGACCTCCGGTGATAcca     >  2:193078/1‑142 (MQ=255)                                                                                                                                     tgATGTCGGTTGTCTGGAATTGATCCACGGGCCAACGCTGGCATTTAAAGAGGTCGGCGGTCGCTTTATGGCACGAATGCTGACCGATATGGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAg  <  1:494207/142‑1 (MQ=255)                                                                                                                                        |                                                                                                                                            GAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAG  >  NC_000913/3874‑4148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑