Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	468,288	A→T	57.8%	K79* (AAG→TAG)	glnK →	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	468,288	0	A	T	57.8%	0.1 / 47.2	38	K79* (AAG→TAG)	glnK	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base A (7/9);  new base T (12/10);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 7.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.39e-02

CACCGAAGTGAAAGGTTTCGGGCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGAAAAATGAAGATA  >  CP009273/468143‑468430                                                                                                                                                   |                                                                                                                                               cACCGAAGTGAAAGGTTTCGGGCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAgg                                                                                                                                             <  1:850216/149‑1 (MQ=255)     gAAGTGAAAGGTTTCGGGCGTCACCACACTGGGT‑CCAATCTGTAGCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGCAGTGATCGATATCGTCGGTAAcgcgtt                                                                                                                                         <  1:397481/149‑3 (MQ=255)     gAAGTGAAAGGTTTCGGGCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAggcggc                                                                                                                                         <  2:104731/149‑1 (MQ=255)      aaGTGAAAGGTTGCGGGCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCt                                                                                                                                        <  1:220211/149‑1 (MQ=255)                  tCGGGCGTCA‑CAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTGAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGaaaa                                                                                                                            <  1:478062/149‑1 (MQ=255)                     ggCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAAtt                                                                                                                         >  1:736262/1‑149 (MQ=255)                              aaaGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGGGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTCCACCGGAAAAATTGGCgcagg                                                                                                                 >  1:382666/1‑145 (MQ=255)                                 gtgcctGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCCACTCGAGGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCaa                                                                                                              <  1:313877/144‑1 (MQ=255)                                 gggCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCaa                                                                                                              <  2:775795/149‑1 (MQ=255)                                  ggCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGGaaa                                                                                                             >  2:236934/1‑149 (MQ=255)                                  ggCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCaaa                                                                                                             >  2:246047/1‑149 (MQ=255)                                      tGCCGAGCTCTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGCCCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCt                                                                                                         <  1:697253/149‑1 (MQ=255)                                           aGCTGTACCGGGGGGCGGAATACCGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTtcgtc                                                                                                    <  2:505846/149‑1 (MQ=255)                                                                aCAGCGTCAATTGCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCatt                                                                               <  2:88283/149‑1 (MQ=255)                                                                               tGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGc                                                                <  2:664795/149‑1 (MQ=255)                                                                                gCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGCGCGATATCGTCAGTTAGCCGGCTTACCCCGGAAAACTTGGCGACGGCAAAAGCTTCGTCGCTGAATTGCAACGCGTCATACGTCGTCGCACCGGcc                                                               >  1:256545/1‑148 (MQ=255)                                                                                 ccAACAGTAAAAATGCAGGGCGGGATTGCTGATGAACAACTCTATGAAGTGATCCATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGa                                                              <  1:6403/149‑1 (MQ=255)                                                                                     aaGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGcc                                                          <  1:78251/149‑1 (MQ=255)                                                                                        tAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCcgac                                                       >  2:746000/1‑149 (MQ=255)                                                                                          aaaaTTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACAGGCGAAGCcgacga                                                     >  2:150802/1‑149 (MQ=255)                                                                                          aaaaTTGATGGGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCcgacga                                                     <  2:711675/149‑1 (MQ=255)                                                                                             aTTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCCTTCGTATTCGTTCCGGCGCAGCccaccagac                                                  >  2:228226/1‑144 (MQ=255)                                                                                                   gtgGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCt                                            >  2:302590/1‑149 (MQ=255)                                                                                                   ggggCGATTGCGGGTTACCAACGCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCt                                            <  2:758516/147‑1 (MQ=255)                                                                                                         aTTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAAtc                                      >  1:852829/1‑149 (MQ=255)                                                                                                              tgatgaCCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATGCGTATTCGTACAGGCGAAGCGGACGAAGCGGCGCGGTAATATCTgg                                 >  1:575832/1‑149 (MQ=255)                                                                                                              tgatgaCCAACTCGATGAAGTGATCGATATCGTCAGTTAGGCGCCTTACACCGGAAAAATCGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATCCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGCAATCCCTgg                                 >  1:244865/1‑149 (MQ=255)                                                                                                                         ttgATGAAGTCACCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCTTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAAc                      <  1:387652/147‑1 (MQ=255)                                                                                                                         tCGAGGAAGTCATCGACATCGTCAGTTAGGAGAATAAAAACAGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAAc                      <  1:524473/149‑1 (MQ=255)                                                                                                                           gATGAAGTGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAg                    >  1:101105/1‑149 (MQ=255)                                                                                                                            aTGACGGGATCGATCTCGTAAGTTAGCCGGCTTACACCGGAAAAATTGGCTGCGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAgg                   <  1:678493/149‑1 (MQ=255)                                                                                                                                 gTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAGTCTTCGTCGCTGCATTGCGACGCGTCATTCGTCTTCGGACCGGCGAAGCCGACGACACGGCGCTGTAATCTCTGGCACCCAGCAACATGACCGa              >  1:43198/1‑149 (MQ=255)                                                                                                                                  tGATCGATATCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGaa             >  2:543408/1‑149 (MQ=255)                                                                                                                                    aTCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGaaaa           >  1:262482/1‑149 (MQ=255)                                                                                                                                    aTCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGaaaa           >  2:686633/1‑149 (MQ=255)                                                                                                                                         tatCGTCAGTTAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGAAAAATGaa      <  1:509457/149‑1 (MQ=255)                                                                                                                                           tCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTACACTCTGGCACACACCAACAGGAACGCACAATCAAGa    >  1:45044/1‑149 (MQ=255)                                                                                                                                             gTCAGTTAGGCGGCTTACACCGAAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCGGTAATCTCTGGCACACAGCAACAGGAACggacaaggacgaga  >  1:374115/1‑136 (MQ=255)                                                                                                                                                   |                                                                                                                                               CACCGAAGTGAAAGGTTTCGGGCGTCA‑GAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACGGCAAAATCTTCGTCGCTGAATTGCAACGCGTCATTCGTATTCGTACCGGCGAAGCCGACGAAGCGGCGCTGTAATCTCTGGCACACAGCAACAGGAACGAAAAATGAAGATA  >  CP009273/468143‑468430

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: ‑