Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	2,440,860	C→A	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	97.4%	121.2 / NA	39	P31P (CCG→CCT)	aroC	chorismate synthase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (18/19);  total (20/19)
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

CGGTAGTAACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCG  >  CP009273/2440721‑2441005                                                                                                                                            |                                                                                                                                                  cGGTAGTAACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCa                                                                                                                                          >  2:325207/1‑149 (MQ=255)     agtaACGCCTTCAAAAACTCCGGAGAGTATTTTCACCTGCTAAGAAATCCAGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATcga                                                                                                                                      <  2:646748/149‑1 (MQ=255)      gtaACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGGGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGCGGTGATGTTGCAGATCCCCTGCCGTCAGCGGAATGCCGGGTGGAACACCAAcgat                                                                                                                                     >  1:664964/1‑148 (MQ=255)      gtaACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGCTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATcgac                                                                                                                                     <  1:658508/149‑1 (MQ=255)         aCGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGAt                                                                                                                                  <  2:831473/149‑1 (MQ=255)         aCGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGAt                                                                                                                                  <  1:682800/149‑1 (MQ=255)         aCGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGAGGAAGAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCACGTTGCAGGTACGCTGCCGGCAGCGGAAGGACTGGAGGGacacacgagacgat                                                                                                                                  >  1:721843/1‑139 (MQ=255)             cTTCAAAAACACCGGAGAGAAGTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAg                                                                                                                              <  2:773724/149‑1 (MQ=255)               tCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGcc                                                                                                                            >  2:846415/1‑149 (MQ=255)               tCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGcc                                                                                                                            >  2:846383/1‑149 (MQ=255)               tCAAAAACACCGGAGAGAATTTTGACCGGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGcc                                                                                                                            <  2:43524/149‑1 (MQ=255)                       acCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCa                                                                                                                    >  1:771315/1‑149 (MQ=255)                           gagagaATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGccc                                                                                                                <  1:855708/149‑1 (MQ=255)                                      gACCTGATCCGGCTCGCGGCGCGGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCAATTcac                                                                                                     <  1:774508/149‑3 (MQ=255)                                       aCCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCCCGCTGTCCCAGGGCGACGACGGTCGAGGTAAGGTTGCAGGGACGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCCACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGcc                                                                                                    >  1:246087/1‑149 (MQ=255)                                           gATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAg                                                                                                <  2:624258/149‑1 (MQ=255)                                            aTCCGACTCGCGGCGCTGGGGGGTATAGCGCGATGGCCCAGGGCGACGACGGTCGAGGTGATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCCGCGCGTGAGATTCGCCCAAgg                                                                                               >  1:244563/1‑149 (MQ=255)                                              ccGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAggtg                                                                                             <  1:325207/149‑1 (MQ=255)                                                         cgcTCGGCGGTACAGCGCCATGTCCCAGGGCGACGACCGTCGAGTTCATGTTCCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACTATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGaaa                                                                                  <  2:707847/149‑1 (MQ=255)                                                                   tataGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCa                                                                        <  2:771315/149‑1 (MQ=255)                                                                    ataGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGGATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCaa                                                                       <  2:843964/149‑1 (MQ=255)                                                                                cccAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCGTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAg                                                           <  2:294654/149‑1 (MQ=255)                                                                                 ccAGGGCGACGACGGTCGAGGTCTTGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGGCGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGc                                                          >  2:498210/1‑149 (MQ=255)                                                                                       cggcgacgGGCGAGGACGTGGTGCAGGGCCGCTTCCGTCAGCGGAATGCCTGGAGGAACGCCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCAc                                                    >  1:658168/4‑149 (MQ=255)                                                                                           gacgGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCCGCCATCACGGCt                                                >  2:785780/1‑149 (MQ=255)                                                                                           gacgGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGCTGAACAAATGGGTTTCAACCCATCACgcgt                                                >  2:644836/1‑146 (MQ=255)                                                                                            acgGTCGAGGTCATGTTGCAGTTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTc                                               <  2:87268/149‑1 (MQ=255)                                                                                              ggTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTAc                                                                                        >  1:401963/1‑106 (MQ=255)                                                                                              ggTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTAc                                                                                        <  2:401963/106‑1 (MQ=255)                                                                                                  gAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTAt                                         <  2:667851/149‑1 (MQ=255)                                                                                                      tCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAACGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTAttgtt                                     >  1:539013/1‑149 (MQ=255)                                                                                                           ttGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGCGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGtt                                >  2:445710/1‑149 (MQ=255)                                                                                                             tcatgTCGGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTg                              <  1:741986/145‑1 (MQ=255)                                                                                                             gCAGGTCCGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATCGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTg                              >  1:428570/1‑149 (MQ=255)                                                                                                                    cGCTTCCGTCAGCGGAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGGTTCGCCGAAGGTGGTTACGCGAAAGCGTCGTCCAATTGTGTTTCCCGCCATCACGGCTCCGGTATGGTTGTGTTTGCGTGttt                       >  2:190192/1‑149 (MQ=255)                                                                                                                                 ggAATGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTtat          <  1:517605/149‑1 (MQ=255)                                                                                                                                    aTGCCTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGACGCAGGTTGGGACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTGAATCTTTATaaa       >  2:791519/1‑149 (MQ=255)                                                                                                                                       ccTGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCATGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATcg    >  2:6532/1‑149 (MQ=255)                                                                                                                                         tGGAGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATcgcg  >  1:715327/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                  CGGTAGTAACGCCTTCAAAAACACCGGAGAGAATTTTGACCTGATCCGGCTCGCGGCGCTGGGTGGTATAGCGCGATGTCCCAGGGCGACGACGGTCGAGGTCATGTTGCAGGTCCGCTTCCGTCAGCGGAATGCCTGGCGGAACACCATCGACGATGCAGCCGAGCGCCAGCCCGTGCGATTCGCCGAAGGTGGTTACGCGAAAGAGTTGTCCAATTGTGTTTCCAGCCATCACGGCTCCGTTATTGTTGTGTTTGCGTGTTTACTTAATCTTTATAAATCGCG  >  CP009273/2440721‑2441005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑