Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,054,744	G→C	49.8%	T224R (ACG→AGG)	nac ←	nitrogen assimilation regulon transcriptional regulator; autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,054,744	0	G	C	49.8%	1.4 / 15.5	16	T224R (ACG→AGG)	nac	nitrogen assimilation regulon transcriptional regulator; autorepressor
Reads supporting (aligned to +/- strand):  ref base G (5/3);  new base C (4/4);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGCGCAATAGCATTCACA  >  CP009273/2054606‑2054875                                                                                                                                           |                                                                                                                                    aaaTTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGTTGATTCGGGTAATTCTGCAACGTTCATGCCGCTGGCAATCGCTGCGGTAAGCCTGGCAATAGa                                                                                                                           <  2:53040/149‑1 (MQ=255)                  gagaCTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTACGACTGGCCATAGACTCAAATTCAcc                                                                                                               >  1:85676/1‑144 (MQ=255)                      cTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTAGCAATCGCTGCGGGAAGCGTGGCAATCGACCCAATTTCACCAATa                                                                                                           >  1:96623/1‑144 (MQ=255)                           ggAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCCATTTCACCAATAACttt                                                                                                      >  1:198131/1‑144 (MQ=255)                              aGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGAGTAATACTGCAACGCCCATGCCGCTGGTAATCGCTGCGGTAAGCCTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGa                                                                                              <  2:265085/149‑1 (MQ=255)                                              gACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCCTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGaaaa                                                                              <  2:124652/149‑1 (MQ=255)                                               aCATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGTCTTATTTTTACCAATAACTTTTGCCGTGAGTCGCCGTAGGGaaaaa                                                                             <  2:65729/149‑1 (MQ=255)                                                 aTCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGc                                                                           >  2:244888/1‑149 (MQ=255)                                                              cTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCaa                                                                   >  1:252993/1‑144 (MQ=255)                                                                                                 aaTACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAAGAGCACTGTAATCACTGGGGAGAAagag                           <  2:107323/149‑1 (MQ=255)                                                                                                     cTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCCTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGAAATCACTGGGGAGAAaga                            >  1:20359/1‑144 (MQ=255)                                                                                                         aaCGCCCATGCCGCTGGCAATCGCTGCGGTAAGCCTGGCAATAAACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCCCTGGGGAGAAAGAGGTTCAttt                   >  2:209557/1‑149 (MQ=255)                                                                                                               cATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGCGCaa             >  2:146363/1‑149 (MQ=255)                                                                                                                        ggCAATCGCGTCGGTAAGCGTGGCAATAGACTCAATTTCACCAAGAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGCGCAATAGc         <  1:216646/144‑1 (MQ=255)                                                                                                                              gccTGCGGTAAGCCTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGCGCAATAGCATTcac   <  1:252875/142‑1 (MQ=255)                                                                                                                               gCTGCGGTAAGCCTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGGGCAATAGCCTTcaca  >  1:27519/1‑144 (MQ=255)                                                                                                                                           |                                                                                                                                    AAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCGGCCGATTCGGGTAATACTGCAACGCCCATGCCGCTGGCAATCGCTGCGGTAAGCGTGGCAATAGACTCAATTTCACCAATAACTTTTGCCGTGAGTCGCCGTAGGGAAAAAGCCTCATCAACACGAAGTCTAATAGCACTGTAATCACTGGGGAGAAAGAGGTTCATTTGCGCAATAGCATTCACA  >  CP009273/2054606‑2054875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑