Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,069,743	C→T	A33T (GCA→ACA)	rutG ←	pyrimidine:H(+) symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,069,743	0	C	T	94.1%	86.7 / ‑5.2	35	A33T (GCA→ACA)	rutG	pyrimidine:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (23/9);  total (24/11)
Fisher's exact test for biased strand distribution p-value = 5.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.12e-01

ATATTCGGGTTAATGCCCTGACCGTTAAAGCCCGTCGCGGCGATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGCCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCG  >  NC_000913/1069514‑1069965                                                                                                                                                                                                                                       |                                                                                                                                                                                                                               atatTCGGGTTACTGCCCTGACCGTTAAAGCC‑GTCGCGGCGATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCCATCGt                                                                                                                                                                                                          >  1:311616/1‑251 (MQ=255)                          tAAAGCCCGTCGCGGCGATCACCACGACGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACAACGCCCCCCCGTGTTGAACGCCCATTCCTGTCATCTGAGCAAACGGCAATCGTTCATCCGGTGCGACCACGCCGctc                                                                                                                                                                                  >  2:54818/1‑251 (MQ=255)                            aaGCCCGTCGCGGCGATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCCGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTTTGAGCAACAGCCAATCGTTCATCCGGCGAGAcacccccgccccc                                                                                                                                                                                >  2:311823/1‑239 (MQ=255)                                 cGTCGCGGCGATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGACCCATCAGAATCGGCATTAACACC‑ATCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGt                                                                                                                                                                             >  2:321947/1‑249 (MQ=255)                                          gATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGAtt                                                                                                                                                                  >  1:316412/1‑251 (MQ=255)                                             caccacGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGAtttt                                                                                                                                                                >  2:213203/1‑250 (MQ=255)                                                     cGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAGGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGAGTTGAACGCCCATTCCTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGCCCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGcc                                                                                                                                                         >  2:309494/1‑249 (MQ=255)                                                       aCAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCACATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGGGGTCGATTTTAACTGCCCGTg                                                                                                                                                     >  2:158742/1‑251 (MQ=255)                                                              ccGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAggcaa                                                                                                                                               >  1:48233/1‑247 (MQ=255)                                                                            aaaaactggggctccccccccccgGTAATAAAGAAAAACAGTAACGTGCCGACCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACCCC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGCCGTCTGAGCAAACGGCAACCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCAt                                                                                                                                <  1:370960/230‑1 (MQ=255)                                                                                        aCGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGCGGTCGATTTTAACTGCCAGTGAGGTAAACCGAACATTGCCATCAGCTGTCTCCt                                                                                                                    >  2:362429/1‑251 (MQ=255)                                                                                                         aaaGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCCGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAAc                                                                                                                                                                                                                   >  2:407189/1‑139 (MQ=255)                                                                                                         aaaGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAAc                                                                                                                                                                                                                   <  1:407189/139‑1 (MQ=255)                                                                                                            aaaaaccataaacgaccctaTCCCCGACATTAAAAGGGAAAGATTGGGATCCATCCCCAACAGAATCGGCATTAACCCC‑GTCGCGCCAAACATCGCCCCCGCGTGTGGAACGCCCATTACTTTCGTCTGAGCAACCGGCAATCGTTCATCCGGCGCGCCCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAgg                                                                                                <  1:204716/232‑1 (MQ=255)                                                                                                                   aGTACCGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACAGCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGCCCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATc                                                                                         <  1:288066/251‑1 (MQ=255)                                                                                                                    gTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGGTAACAAGCAGGGCGCATc                                                                                         >  1:326304/1‑250 (MQ=255)                                                                                                                     aaaCGTGCCGACCCCCGACATAAAAATGGAAAGATTGGGATCCAGCCCCATCAGAAGCGGCATTAACCCC‑GTCGCGCAAAACTCCGCCACCGCGTGTTGAACGCCAATTACTGTCGGCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAg                                                                                       <  1:362429/250‑1 (MQ=255)                                                                                                                       ccgtcccGACCCCCGACATTAAAATGGAAAGATGGTGATCCAGCCCCATCACAAGCGGTATTAAACCC‑GTCGCGCCAAACACCGCCACCGCGTGTTTAACCCCCATTACTGTCGTCTGATCAAACGGCAATCGTTCATCCGGCGCGCCCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAgcg                                                                                     <  1:27917/246‑1 (MQ=255)                                                                                                                           gccaaaccccGACATTAAAAGGGAAAGATTGGGATCCAGCCCCATCAGAACCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTg                                                                                 <  1:380323/245‑1 (MQ=255)                                                                                                                             cGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGAt                                                                               >  1:220008/1‑251 (MQ=255)                                                                                                                                  cccGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTg                                                                          >  1:283559/1‑251 (MQ=255)                                                                                                                                   ccGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGc                                                                         <  1:311823/251‑1 (MQ=255)                                                                                                                                     gACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGCATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCg                                                                        >  1:328029/1‑250 (MQ=255)                                                                                                                                           aaaaTGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGAGTTGAACGCCCATTACTGCCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAACCCGACCCTTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCCTCAGCGCGTGCTCACCGCGATCGAAc                                                                 >  2:141427/1‑251 (MQ=255)                                                                                                                                                    agttggggctcccgCCCCCTCAGAAGCGG‑AATAACACCCGTCGCGCCAAACATCGCCACCGCTGGTTGAACGCCCATTACTGGCGTTTGAGAAAACGGCAATCGTTCTCCCGGCGCGCCCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGc                                                        <  2:316412/238‑1 (MQ=255)                                                                                                                                                         gggACCCAGCCCCATCAGAATCGGCATAAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGCCTGAGCAAACGGCAATCTTCCACCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTa                                                   <  1:211120/251‑1 (MQ=255)                                                                                                                                                                     cATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGgtggggtgtg                                       >  2:352620/1‑251 (MQ=255)                                                                                                                                                                         aGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGGGACgg                                   >  1:67494/1‑250 (MQ=255)                                                                                                                                                                                 cATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGc                           >  2:395538/1‑251 (MQ=255)                                                                                                                                                                                   ttAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCtt                         >  1:156560/1‑251 (MQ=255)                                                                                                                                                                                     aaCACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGCGAGGAAAACCGAACATTGCCATCCGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCg                       >  2:48860/1‑251 (MQ=255)                                                                                                                                                                                                 gcCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCaaa             >  1:400268/1‑250 (MQ=255)                                                                                                                                                                                                  ccAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTATAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAAc                                                                 <  2:126664/197‑1 (MQ=255)                                                                                                                                                                                                  ccAAACATCGCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTATAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAAc                                                                 >  1:126664/1‑197 (MQ=255)                                                                                                                                                                                                           gCCACCGCGTGTTGAACGCCCATTACTGTCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCg  >  1:265841/1‑251 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                               ATATTCGGGTTAATGCCCTGACCGTTAAAGCCCGTCGCGGCGATCACCACGCCGACAAAAGCCGCGCTGGAGCCGAGATAACTGGGGACGCGCCCGCCGGTAATAAAGAAAAACAGTAACGTGCCGATCCCCGACATTAAAATGGAAAGATTGGGATCCAGCCCCATCAGAATCGGCATTAACACC‑GTCGCGCCAAACATCGCCACCGCGTGTTGAACGCCCATTACTGCCGTCTGAGCAAACGGCAATCGTTCATCCGGCGCGACCACGCCGCTCTCTGTAGAGGTCGATTTTAACTGCCAGTGAGGAAAACCGAACATTGCCATCAGCTGTCTCCTTAAGGAGGTTAACAAGCAGGGCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCG  >  NC_000913/1069514‑1069965

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑