Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,440,860	C→A	54.6%	P31P (CCG→CCT)	aroC ←	chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,440,860	0	C	A	54.6%	‑2.1 / 26.6	26	P31P (CCG→CCT)	aroC	chorismate synthase
Reads supporting (aligned to +/- strand):  ref base C (9/3);  new base A (10/4);  total (19/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.18e-01

AGTAACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCGAA  >  CP009273/2440725‑2441007                                                                                                                                        |                                                                                                                                                    agtaACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGGCATGTTGCCGGTCCTCTTCCGTCAGCGGAATGCCTGGAGGGAAACCATcga                                                                                                                                        >  2:99094/1‑149 (MQ=255)      cGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATg                                                                                                                                   <  2:53525/149‑1 (MQ=255)       gCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGGCGAGGTCATGTGGCATTTCCTCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGc                                                                                                                                  >  2:205157/1‑149 (MQ=255)          ttCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGc                                                                                                                               >  1:265072/1‑149 (MQ=255)                 acacCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACCACGGTCGAAGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACCCCATCGACGATGCAGCCGAgcgc                                                                                                                        >  2:29214/1‑149 (MQ=255)                                 tGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGATGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGTACGCCTGGCGGAACACCATCGGCGATGCGGCCGAGCGCCAGCCCGTGCGATACg                                                                                                        >  1:196923/1‑149 (MQ=255)                                 tGACCTGATCCGGCTCGCGGCGATGGGAGGTAAAGCGCGATGGCCCAGGGCGGCGACGATCGAGGGCATGTTGCCGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCTCCAGCCCGTGGGACTCg                                                                                                        >  1:122420/1‑149 (MQ=255)                                         tCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCCTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAggt                                                                                                <  1:220939/149‑1 (MQ=255)                                          ccGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTACGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAggtg                                                                                               >  1:129120/1‑149 (MQ=255)                                              acggcggcgCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGGCATGTTGCAGGGCCGCTTCCGTCAGCGGAATGCCTGGAGGGACACCATCGACGATGCAGCCGAGCGCCAGCCCGGGCGATTCGCCGAAGGTGGTTa                                                                                           >  1:261631/4‑149 (MQ=255)                                                        tGGGGGGGATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAagag                                                                                 >  1:299949/1‑149 (MQ=255)                                                                             ccAGGGCGACGACGGTCGAGGACATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCCTCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGGTGTCCAATTGTGCTTCCaac                                                            >  1:48379/1‑147 (MQ=255)                                                                              cAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGGGTTGTCCAATTGTGTTTCCAGcc                                                           >  2:145458/1‑149 (MQ=255)                                                                              cAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGcc                                                           >  2:236967/1‑149 (MQ=255)                                                                                          ggTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCGTCCCGGCTCCg                                               >  2:106180/1‑149 (MQ=255)                                                                                               aGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTAtt                                          >  2:300041/1‑149 (MQ=255)                                                                                               aGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAAAGATGTCCAAGTGTGGTTCCAGCCATCACGGCTCCGtgctt                                          >  1:187839/1‑145 (MQ=255)                                                                                                    aTGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATtgttgt                                     <  1:311579/149‑1 (MQ=255)                                                                                                                      cGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTaa                   <  1:265541/149‑1 (MQ=255)                                                                                                                       gTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAAt                  <  2:353297/149‑1 (MQ=255)                                                                                                                                aTGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAAACTTAATaaa         >  1:298294/1‑149 (MQ=255)                                                                                                                                aTGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTGATTGTTGTGTTTGCGTGTTTACTTAATCTTTATaaa         >  1:349115/1‑149 (MQ=255)                                                                                                                                   ccTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATcg      >  2:333908/1‑149 (MQ=255)                                                                                                                                   ccTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATcg      <  1:65693/149‑1 (MQ=255)                                                                                                                                   ccTGGAGGAACACCATCGACGATGCAGCCGAGCACCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTGTCCAGCCATCACGGCTCCGTTATTGTTGTGTTCGGGTGTTTACTTAATCTTTATAAATcg      >  2:261346/1‑149 (MQ=255)                                                                                                                                      gccGGAACACCCCCGACGACGCCGCCGGGCGCCAGCCCGTGCCATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCGa   <  2:120415/147‑1 (MQ=255)                                                                                                                                       gCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCGaa  <  2:299949/149‑1 (MQ=255)                                                                                                                                        |                                                                                                                                                    AGTAACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCGAA  >  CP009273/2440725‑2441007

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: ‑