Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,266,469	C→A	L199F (TTG→TTT)	tdcA ←	DNA‑binding transcriptional activator TdcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,266,469	0	C	A	94.1%	110.8 / NA	34	L199F (TTG→TTT)	tdcA	DNA‑binding transcriptional activator TdcA
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base A (17/15);  total (19/15)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

CGACCATACCGCGGCATATTGTGCCACAGGTAATGTTTCTTCAACCGGAATAGTAATAAATTGATTAGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑CAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGAACACCTCTTTGAACTT  >  NC_000913/3266232‑3266714                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                      cGACCATACCGCGGCATATTGTGCCACAGGTAATGTTTCTTCAACCGGAATAGTAATAAATTGATTAGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCTCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTgt                                                                                                                                                                                                                                           <  1:126255/250‑1 (MQ=255)     cATACCGCGGCATATTGTGCCACAGGTAATGTTTCTTCAACCGGAATAGTAATAAATTGATTAGAAACAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTgttcgtt                                                                                                                                                                                                                                      >  1:134466/1‑251 (MQ=255)                                                    aGTAATAAATTGATTAGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGAGTGGTGGTGCCGGTGCATGTTCggg                                                                                                                                                                                             >  1:149886/1‑245 (MQ=255)                                                    aGTAATAAATTGATTAGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTGCGTTCGTCAACGACTCCAGCGTGGTGGTGCCGTTGCATGTTCggg                                                                                                                                                                                             <  2:149886/245‑1 (MQ=255)                                                                   aGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACaa                                                                                                                                                                        <  1:56635/251‑1 (MQ=255)                                                                     aacaaaaaGGCGACGTCATATCACAAGGAATTACAGTTAAGAACTCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAAAGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAAc                                                                                                                                                                      >  2:272196/5‑251 (MQ=255)                                                                      aCCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACt                                                                                                                                                                     <  1:16538/251‑1 (MQ=255)                                                                         aaaaGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGttctt                                                                                                                                                                                                                                   >  1:131716/1‑186 (MQ=255)                                                                         aaaaGGTGACGTCAGATCACAAGGAATTACAGTTAAGAAATCAGCATGGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCAGTAGTACCCCAGATTAGTTTGGGG‑AAACACCCACTGTTCGttctt                                                                                                                                                                                                                                   <  2:131716/186‑1 (MQ=255)                                                                                gACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGa                                                                                                                                                            >  1:118800/1‑250 (MQ=255)                                                                                  cGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAAc                                                                                                                                                          >  1:114060/1‑250 (MQ=255)                                                                                    tCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGCCAGTTTTAAGGATGCTTTCAATCCTAACGCTATTTATTTGTAACGAAGAAAGCACTTCGCTGAAGGACCCCATATTAGTTTGTGG‑AATCACCCACTGTTCGTTCTTCAACGCCTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGCCTTAATGGCTACCAGCACAAACTCGGACTCGAAc                                                                                                                                                          >  1:189855/1‑248 (MQ=255)                                                                                               ggAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATg                                                                                                                                            >  2:17265/1‑251 (MQ=255)                                                                                                       aGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGGTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCt                                                                                                                                    <  2:96495/251‑1 (MQ=255)                                                                                                              aaaTCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCtt                                                                                                                             >  1:265487/1‑251 (MQ=255)                                                                                                                  cAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTGTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCAtt                                                                                                                         <  1:72374/251‑1 (MQ=255)                                                                                                                                       aaaTTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGAAGTTCGCTGTAGTACCCCATAATAGTTTGTGG‑CAACACACACTGTTCGTTCTTCAACGAATCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCAGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGATTCATTTCTGCACTTAACGAACCAATc                                                                                                    >  1:293214/1‑251 (MQ=255)                                                                                                                                       aaaTTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAAGACTGATGCTATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTTCATCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACGTGCACAATCTCTTACGCGATCAGCGGCTTAACATGTAAAGTCTGGATCGTCATTGCTGCACTTAACTTTCCAAt                                                                                                     <  2:45223/250‑1 (MQ=255)                                                                                                                                              cACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAAt                                                                                             <  2:265487/251‑1 (MQ=255)                                                                                                                                               aCGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCgg                                                                                                                                                     <  1:148025/194‑1 (MQ=255)                                                                                                                                               aCGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCgg                                                                                                                                                     >  2:148025/1‑194 (MQ=255)                                                                                                                                                         cGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGGAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTTTTCGTTCTTCAACGACTCCAGCGTGGTGGGGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTGCCAATCGCAAAATCCAGTCGAcc                                                                                   <  2:292342/250‑1 (MQ=255)                                                                                                                                                                 aCGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGCCTCGCACAGCGGCTCAACATGTAAATCCTGAAGCTTCCTTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCTTCGCGGAt                                                                          >  2:238943/1‑251 (MQ=255)                                                                                                                                                                                                        gtaAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTAGTTCTTCAACGACTCCAGCGTGGTGGTGACGGTGCATGTTCGGGACTTACTGGCTACCAGCAAAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTAGCGGATTGACGGTAAGAACGAAGACAGTTGCGCTTaatacat                                      >  1:40845/1‑248 (MQ=255)                                                                                                                                                                                                          aaGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACGCCCACTGTTCGGTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGaa                                  <  1:101115/250‑1 (MQ=255)                                                                                                                                                                                                           aGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACGTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAAc                                <  1:129682/251‑1 (MQ=255)                                                                                                                                                                                                                   gCTGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCtt                        <  1:237001/251‑1 (MQ=255)                                                                                                                                                                                                                    cTGTAGTACACCATATTAGTTTGTGGACAA‑ACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCATGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGTCCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCttt                       >  2:306910/1‑251 (MQ=255)                                                                                                                                                                                                                     tGTAGTACCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTc                      >  1:177911/1‑251 (MQ=255)                                                                                                                                                                                                                          taCCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGCCTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGa                  >  1:128226/1‑250 (MQ=255)                                                                                                                                                                                                                          taCCCCATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGa                  >  1:34726/1‑250 (MQ=255)                                                                                                                                                                                                                             cccATATTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGCacac              >  2:89742/1‑251 (MQ=255)                                                                                                                                                                                                                                 tatTAGTTTGTGG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGAACACctct          >  1:127837/1‑251 (MQ=255)                                                                                                                                                                                                                                          gtgG‑AAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATGGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGAACACCTCTTTGAACtt  <  1:272196/250‑1 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                      CGACCATACCGCGGCATATTGTGCCACAGGTAATGTTTCTTCAACCGGAATAGTAATAAATTGATTAGAACCAAAAGGTGACGTCATATCACAAGGAATTACAGTTAAGAAATCAGCATTGAGAACAAGATTATAAATTGTCACGACTGAGTCGGTTTTAACGATGTTTTCAATACTGATGCCATTTCTTTGTAACGTAGTAAGCAGTTCGCTGTAGTACCCCATATTAGTTTGTGG‑CAACACCCACTGTTCGTTCTTCAACGACTCCAGCGTGGTGGTGCCGGTGCATGTTCGGGACTTACTGGCTACCAGCACAAACTCGGACTCGAACAGCGGCTCAACATGTAAATCCTGAAGCTTCATTTCTGCACTTAACGTACCAATCGCAAAATCCAGTCGACCGTCGCGGATTGCCGGTAAGAACGAAGACAGTTGCGCTTCATACATAGAAACCTGCGCTTTCGGGAACACCTCTTTGAACTT  >  NC_000913/3266232‑3266714

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑