Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,834,441	G→T	10.4%	A220E (GCA→GAA)	nepI ←	putative transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,834,441	0	G	T	10.4%	112.8 / 2.3	38	A220E (GCA→GAA)	nepI	putative transporter
Reads supporting (aligned to +/- strand):  ref base G (18/16);  new base T (2/2);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

CGCACTCACAGCCAGTATTAACGGCGCGCCTGCTAAGGCCAGTTTTACCGAACGTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAAGACATTGCGCCAACCGATAAGCTCGCCTAAAAAACTGCCCAACGGCGCGGCAATCACCAGCGCAATAGAAACCGCGCCGAA  >  CP009273/3834215‑3834652                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    cGCACTCACAGCCAGTATTAACGGCGCGCCTGCTAAGGCCAGTTTTACCGAACGTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAATCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTAAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATATTGtccgtat                                                                                                                                                                      >  1:272869/1‑268 (MQ=255)                        gcgcgcCTGCTAAGGCCAGTTTTACCGAACGTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAGGAAAGCAAACTGCACGGCGAAAGACATGAAGATGGCGATAATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGAGaa                                                                                                                                              >  1:323958/1‑275 (MQ=255)                          gcgcCTGCTAAGGCCAGTTTTACCGAACGTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACAGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATCGCGATCATCCCTGCCATCACACACGGACGTTGTAATAAGAGGAAAATATTTTGTTTATGATCAGAGGGAACACCTAGCAGTGaaag                                                                                                                                            >  1:177832/1‑273 (MQ=255)                                                                           gCGACGTACCAATAAAGCTGGCGATACCAAAAATCAACAGCACCAGCGTTAAGCCCACCCCGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATCTACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCAccgccgcc                                                                                           <  1:10481/275‑1 (MQ=255)                                                                                       aggtgCTGGCGATACCAACACTCCACAGCACCAGCGTTAACCCATCCACGCCGAATCCCGCCAGGTTCATATACGCCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAAGACa                                                                               <  2:177825/271‑1 (MQ=255)                                                                                              ggCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTGTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCAAGAAAATACACAGCACGCCCATCACCGCCGCGGAATTAAAGACAtagagc                                                                         >  1:257561/1‑269 (MQ=255)                                                                                                  aTAACAAAACTCAACAGCACCAGCGTTAAGCCAGCCACGCCGAAGCCCGCCAGGTTCATATACAACGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGTCAATGATTTGATAATCCAGAAAATACACAGCa                                                                                                            <  1:314746/235‑1 (MQ=255)                                                                                                                      cAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGCTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCTTGGc                                                                                                                                                    >  1:338818/1‑175 (MQ=255)                                                                                                                             aaGCCATCCACGCCGAATCCCGCCAGGTTCTTATACACCGGGCGAATAGACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCAGCCCGGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAAGACATTGCGCCAACCGATAAGCTCGCCTAAAAAACTGCCCaa                                         <  1:285541/275‑1 (MQ=255)                                                                                                                             aaGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAAGACATTGCGCCAACCAAAAAGCTCGCCNTAAAAACTGCCCaa                                         >  2:376630/1‑275 (MQ=255)                                                                                                                             aaGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCAGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGa                                                                                                                                                                 >  2:173702/1‑155 (MQ=255)                                                                                                                                 cATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCAGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGt                                                                                                                                                             <  1:173708/155‑1 (MQ=255)                                                                                                                                   tCCACGCCGAATCCCGCCAGGTTCATATACACCGTGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGc                                                                                                                                                                                                                    >  1:320720/1‑98 (MQ=255)                                                                                                                                       cGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATc                                                                                                                                                                                                                <  2:320708/98‑1 (MQ=255)                                                                                                                                               cccgcccgGTTCATATAAACCGGGCTAATATACTGTATAAAAGCAAACTGCCCGGCGACAGACATGAAGATGGCGATCATCCCGGCCATCANACCCGGACGTTGTAATAAACGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAATACATTGCGCCAACCGTTAAGCTCGCCTAAACAACTGCCCAACTGCGCGGCAATCACCAg                       <  1:376642/275‑1 (MQ=255)                                                                                                                                                                 acCGGGCGAATATACGTGAAGAAAGCGAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCacac                                                                                                                                                                                                            >  1:336938/1‑76 (MQ=255)                                                                                                                                                                 acCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTTCCATCACACCCGGACGTTGTAATAAGCGGAAAGTAtttt                                                                                                                                                                              >  1:440627/1‑106 (MQ=255)                                                                                                                                                                 acCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAg                                                                                                                                                                                           >  1:286599/1‑93 (MQ=255)                                                                                                                                                                     ggCGACTATACGTGAAGAAAGCAAACTGCACGGCGAAAGACATGAAGATGGCGATCATCACTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGCGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTCAAGACAtta                                                                            >  1:21507/1‑199 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTg                                                                                                                                                                                                                     >  2:390896/1‑63 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTTCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGttt                                                                                                                                                                          <  2:440611/106‑1 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCgg                                                                                                                                                                                                        <  2:336926/76‑1 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGa                                                                                                                                                                                       <  2:286588/93‑1 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTc                                                                                                                                                           >  1:33700/1‑121 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGa                                                                                                                                               >  2:393097/1‑133 (MQ=255)                                                                                                                                                                     ggCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGNCGCATTAANGACATTGCGCCAACCGATAAGCTCGCCTAAAAAACTGCCCAACGGCGCGGCAATCACCAGCGCAATAGAAACCGCGCCGaa  >  1:344967/1‑274 (MQ=255)                                                                                                                                                                         aaTATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCAt                                                                                                                                                                                                                 <  1:390911/63‑1 (MQ=255)                                                                                                                                                                         aaTATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCt                                                                                                                                                       <  2:33700/121‑1 (MQ=255)                                                                                                                                                                         aaTATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGc                                                                                                                                           <  1:393112/133‑1 (MQ=255)                                                                                                                                                                                gTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGa                                                                                                                                                                                                       >  2:247710/1‑66 (MQ=255)                                                                                                                                                                                    agaaAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGtt                                                                                                                                                                                                   <  1:247719/66‑1 (MQ=255)                                                                                                                                                                                        aGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGc                                                                                                                                                                                          >  1:154422/1‑71 (MQ=255)                                                                                                                                                                                            aaCTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGaa                                                                                                                                                                                      <  2:154419/71‑1 (MQ=255)                                                                                                                                                                                             aCTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAg                                                                                                              >  2:110468/1‑142 (MQ=255)                                                                                                                                                                                                 cccGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACg                                                                                                          <  1:110469/142‑1 (MQ=255)                                                                                                                                                                                                                gAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAg                                                                                                                                                                                           >  2:421336/1‑46 (MQ=255)                                                                                                                                                                                                                    aTGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGa                                                                                                                                                                                       <  1:421351/46‑1 (MQ=255)                                                                                                                                                                                                                      ggCGATCATCCCTTCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGc                                                                                                                                                                   >  1:212732/1‑64 (MQ=255)                                                                                                                                                                                                                          atcatcCCTTCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAgg                                                                                                                                                               <  2:212723/64‑1 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    CGCACTCACAGCCAGTATTAACGGCGCGCCTGCTAAGGCCAGTTTTACCGAACGTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACGTTGTAATAAGCGGAAAGTATTTTGTTTCTGATGCGAGGGTTCGCCTGGCAGTGAAGGCAATGATTTGATAATCCAGAAAATACACAGCACGCCCATCACCGCCGCCGCATTAAAGACATTGCGCCAACCGATAAGCTCGCCTAAAAAACTGCCCAACGGCGCGGCAATCACCAGCGCAATAGAAACCGCGCCGAA  >  CP009273/3834215‑3834652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑