Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,117,280	T→G	S262R (AGC→CGC)	pyrC ←	dihydroorotase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,117,280	0	T	G	88.5%	77.2 / 2.4	26	S262R (AGC→CGC)	pyrC	dihydroorotase
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base G (10/13);  total (11/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.76e-01

GCAAAGCATTCATTTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCTCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCAGTTCACGCAATGCCTGT  >  NZ_CP009273/1117196‑1117368                                                                                     |                                                                                         gcAAAGCATTCATTTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCtt                                                                                     >  1:265502/1‑90 (MQ=255)      gCATTCATTTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCTCTCTTTGCGa                                                                                <  1:122911/90‑1 (MQ=255)      gCATTCATTTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGa                                                                                >  2:568674/1‑90 (MQ=255)       cattcattTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGAt                                                                               <  1:577021/90‑1 (MQ=255)        attcattTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATg                                                                              >  1:764750/1‑90 (MQ=255)                        aCGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCa                                                              <  2:265502/90‑1 (MQ=255)                          ggTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGa                                                            <  2:546669/90‑1 (MQ=255)                          ggTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGa                                                            >  2:108457/1‑90 (MQ=255)                             aGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATc                                                         <  2:406686/90‑1 (MQ=255)                                           gcgcGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATa                                           >  1:318437/1‑90 (MQ=255)                                           gcgcGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATa                                           >  1:962555/1‑90 (MQ=255)                                           gcgcGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATa                                           >  2:160200/1‑90 (MQ=255)                                                        gTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAAcc                              <  1:169639/90‑1 (MQ=255)                                                        gTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAAcc                              >  2:271053/1‑90 (MQ=255)                                                        gTTGAAGCAGCCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAAcc                              <  1:96447/90‑1 (MQ=255)                                                                agcCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGa                      >  1:978348/1‑90 (MQ=255)                                                                 gcCCGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAc                     >  2:577268/1‑90 (MQ=255)                                                                  cccGCGCAGCCGCAACTGCTCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAcc                    <  2:616214/90‑1 (MQ=255)                                                                  cccGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAcc                    <  1:697325/90‑1 (MQ=255)                                                                  cccGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAcc                    <  1:160200/90‑1 (MQ=255)                                                                  cccGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAcc                    <  2:637698/90‑1 (MQ=255)                                                                  cccGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGAcc                    <  2:648655/90‑1 (MQ=255)                                                                   ccGCGCAGCCGCAACTGCTCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCa                   >  2:151693/1‑90 (MQ=255)                                                                   ccGCGCAGCCGCAACTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCa                   <  1:234270/90‑1 (MQ=255)                                                                               aaCTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCAGTTCACGCAATg       <  1:108457/90‑1 (MQ=255)                                                                               aaCTGCGCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCAGTTCACGCAATg       <  1:577268/90‑1 (MQ=255)                                                                                    ctctctTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCAGTTCACGCAATGCCTGt  >  2:429836/1‑90 (MQ=255)                                                                                    ctctctTGCCCATGACGTGCATGCGGCGCAGTACCCGTACCGAGGAATACTCCATTAAAACCGCTGCCGACCAGTTCACGCAATGCCTGt  <  1:882666/90‑1 (MQ=255)                                                                                     |                                                                                         GCAAAGCATTCATTTCTTCAAAGACGGTAGCGTAACTGCCCAGCGCGGTTGGGGCGTTGAAGCAGCCCGCGCAGCCGCAACTGCTCTCTTTGCGATGACGTGCATGTGGCGCAGAATCCGTACCGAGGAATACTCGATTAAAACCGCTGGCGACCAGTTCACGCAATGCCTGT  >  NZ_CP009273/1117196‑1117368

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑