Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,957,805	G→A	L6L (CTG→TTG)	ilvY ←	DNA‑binding transcriptional dual regulator IlvY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,957,805	0	G	A	96.8%	99.7 / ‑3.7	31	L6L (CTG→TTG)	ilvY	DNA‑binding transcriptional dual regulator IlvY
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (9/21);  total (9/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.23e-01

GATCGATGGTGTGGCGCAACTGCTGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAGATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGAATCTGCGCCAGCAGCTGGCACAGCTGGGCAAATGTCGCTTTATGGGCCGCGATGA  >  NC_000913/3957571‑3958049                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                     gATCGATGGGGTGGCGCAACTGCTGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCAGCGCCCGCGCGCTGCGGCCAAAATGGCGTCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCca                                                                                                                                                                                                                                        <  1:51336/249‑1 (MQ=255)      aTGGTGTGGCGCAACTGCTGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGAGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGGTTTCCAATCGCGTAAATcccccaggac                                                                                                                                                                                                                                 >  2:251004/1‑243 (MQ=255)           gtgGCGCAACTGCTGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCCCAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGccc                                                                                                                                                                                                                            >  1:321590/1‑251 (MQ=255)             ggCGCAACTGCTGATACTGCAACAGCGGTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTc                                                                                                                                                                                                                          <  2:103241/251‑1 (MQ=255)                gcAACTGCGGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGAt                                                                                                                                                                                                                       <  2:111529/251‑1 (MQ=255)                      gctgATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTTGTCTCCCGCTTCAGTCAGCTTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCGTGCCGTCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGTCCTCGAAGTTGAc                                                                                                                                                                                                                 <  2:342557/251‑1 (MQ=255)                         gATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGTGACAGCCCTCGATGTTTACGtt                                                                                                                                                                                                              <  1:113550/251‑1 (MQ=255)                         gATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCGTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACg                                                                                                                                                                                                                <  2:326875/249‑1 (MQ=255)                                           gCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAAtgtg                                                                                                                                                                                             >  1:153499/1‑250 (MQ=255)                                              gggCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAGATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGAc                                                                                                                                                                                           <  2:66745/249‑1 (MQ=255)                                                       cgcgCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTAGCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAatat                                                                                                                                                                                <  1:226342/251‑1 (MQ=255)                                                         cgcggcgctTCGCACGCTTCAGTCAGCGTCACCGTGTGGTTATCTCGCACAGACAGCGGCTGACCGAGATCTTCTTCCAGGCGCCTAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCTAAAATGGCTGCTTTCCGCCAGATGCATGAAGGTTTTCAAATCGCGAAAATCCACAGGGACAGCCCTCGATGTTTACGTTGCAAAAATTGCAATGTGACGTAGTGAatatat                                                                                                                                                                              <  1:353703/244‑1 (MQ=255)                                                         cgccgCTCTGCGCCCGGTTCAGGCAGCGTCCCGGTGCGGGTATCGCGCACAAACAGCGGCGGACCGAGATCGTCTTCCAGGCGCTGAAGCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTGCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAatatat                                                                                                                                                                              <  2:304420/247‑1 (MQ=255)                                                                       cGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATa                                                                                                                                                                <  1:341472/251‑1 (MQ=255)                                                                             agtcagCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCCGGAAGGTTTTCAAATCGCGTAAATCCACAGGGAAAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTTTGAATATATCAATTTCCGCAATAAATTTc                                                                                                                                                          >  2:192425/1‑251 (MQ=255)                                                                                               gTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTc                                                                                                                                        <  1:168498/251‑1 (MQ=255)                                                                                                ttATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTc                                                                                                                                        >  1:214116/1‑250 (MQ=255)                                                                                                  aTCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAAt                                                                                                                                     <  1:138032/251‑1 (MQ=255)                                                                                                           aaaCAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTCCCGTACGCCCGTGGATGGGCTCACGTGCATCGCCCGCGCGCTGCGGCCAAACAGGCGGCTTTCCGCCAGATGCCGGAAGGTTTTCAACTCGCGTAAATCCACCGCGACCGCCCTCGATGTTGACATTTCAAACATTGCAATGTGACGTTGTGACTCTATCAATTTCCGCAATAAATTTCCTGTCATATAGTGTATTCCATCTCGCAAAc                                                                                                                            >  2:44654/1‑251 (MQ=255)                                                                                                                   gCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGcgaaccg                                                                                                                    <  2:90242/251‑1 (MQ=255)                                                                                                                     tGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGcgaaccgc                                                                                                                   >  1:118578/1‑249 (MQ=255)                                                                                                                                ttcttcCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGc                                                                                                       >  1:300557/1‑251 (MQ=255)                                                                                                                                    tcCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGca                                                                                                      <  1:48862/248‑1 (MQ=255)                                                                                                                                        ggCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAAGCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAATCACAACATc                                                                                               <  2:340073/251‑1 (MQ=255)                                                                                                                                          cgcTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCAc                                                                                             <  1:271625/251‑1 (MQ=255)                                                                                                                                              gAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCAGATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAg                                                                                          <  2:153499/250‑1 (MQ=255)                                                                                                                                                                   aTGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACtt                                                                    <  1:311776/251‑1 (MQ=255)                                                                                                                                                                             gTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCC‑TCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGa                                                         <  1:5312/251‑1 (MQ=255)                                                                                                                                                                                    gCCCGCGCGCTGCGGCCAAAATGGCGGCTTTACGCCAGATGCAGGAAGGGTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGATGAAGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTACGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGAATCTgc                                                   >  1:72900/1‑251 (MQ=255)                                                                                                                                                                                                                            gCAGGAAGGTTTTCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGAATCTGCGCCAGCAGCTGGCACAGCTGGGCAAATGTCGCTTTATggg           <  1:272880/251‑1 (MQ=255)                                                                                                                                                                                                                                      tttCAAATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGAATCTGCGCCAGCAGCTGGCACAGCTGGGCAAATGTCGCTTTATGGGCCGCGATGa  <  2:165817/250‑1 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                     GATCGATGGTGTGGCGCAACTGCTGATACTGCAACAGCGTTTGCTGGGCGAAAACGCGCAGCTCTTCGCCCGCTTCAGTCAGCGTCACCGTGCGGTTATCGCGCACAAACAGCGGCTGACCGAGATCTTCTTCCAGGCGCTGAATCTGCCGTGAGAGCGTGGATGGGCTAACGTGCATCGCCCGCGCGCTGCGGCCAAAATGGCGGCTTTCCGCCAGATGCAGGAAGGTTTTCAGATCGCGTAAATCCACAGGGACAGCCCTCGATGTTGACGTTGCAAAAATTGCAATGTGACGTTGTGAATATATCAATTTCCGCAATAAATTTCCTGTCATATAGTGAATTCAATCTCGCAAACGCGAACCGAACAATAAGAAGCACAACATCACGAGGAATCACCATGGCTAACTACTTCAATACACTGAATCTGCGCCAGCAGCTGGCACAGCTGGGCAAATGTCGCTTTATGGGCCGCGATGA  >  NC_000913/3957571‑3958049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑