Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,407,204	G→A	intergenic (‑563/‑357)	lrhA ← / → alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,407,204	0	G	A	97.7%	135.4 / ‑4.3	44	intergenic (‑563/‑357)	lrhA/alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (29/14);  total (30/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01

TTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAA  >  NC_000913/2407076‑2407330                                                                                                                                 |                                                                                                                               ttatgttatgTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTAcccc                                                                                                                            <  2:373042/133‑1 (MQ=255)       tatgttaGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGc                                                                                                                      <  1:397771/133‑1 (MQ=255)         tgttaGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGa                                                                                                                    >  2:423620/1‑133 (MQ=255)           ttaGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTATCAATAGTCGCACACCTGACCCTGATTGCGaaa                                                                                                                  >  2:238720/1‑131 (MQ=255)                cAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCg                                                                                                             <  1:451943/133‑1 (MQ=255)                   aGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTTACAATAGTTTCACACCTTACCCCCATTGCGCTACCTCGGaa                                                                                                          >  2:227630/1‑133 (MQ=255)                   aGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGaa                                                                                                          >  1:409054/1‑133 (MQ=255)                          ttctATTATGCATAAGCACATCAATAACTTTTCGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAAtcatca                                                                                                   <  2:235475/133‑1 (MQ=255)                                 attaATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACGCCTTGGAAATCATTACGCAGtt                                                                                            >  1:162801/1‑133 (MQ=255)                                    aataaGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTaaa                                                                                         >  1:476972/1‑133 (MQ=255)                                            caTCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGt                                                                                 >  1:433726/1‑133 (MQ=255)                                             aTCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTa                                                                                >  1:282192/1‑133 (MQ=255)                                             aTCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTa                                                                                >  2:311558/1‑133 (MQ=255)                                             aTCAAAACCGTTTTGTATATTAAACAGTCATTAATTAGCATTATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTa                                                                                <  2:234451/133‑1 (MQ=255)                                               cAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAAt                                                                              >  2:436579/1‑133 (MQ=255)                                                  aaCCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAg                                                                           <  1:436579/133‑1 (MQ=255)                                                       ttttGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAat                                                                      >  1:280457/1‑133 (MQ=255)                                                       ttttGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAat                                                                      >  2:426109/1‑133 (MQ=255)                                                       ttttGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATAACGCAGTAAAATTCTCCGTAAGGAGGAAat                                                                      >  1:136743/1‑133 (MQ=255)                                                         ttGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATTACGCAGTGAAACTCTCTGTAAGGAGGAAatat                                                                    >  2:138296/1‑133 (MQ=255)                                                              tatTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcatca                                                               >  1:479004/1‑133 (MQ=255)                                                               atTAAATAATAATTAATTAGCATCATGCTCATTATTTTATTCCGCTTAACAATACTTTCACACCTTATCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcatcat                                                              >  2:377529/1‑133 (MQ=255)                                                                        taattaatTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCa                                                     <  2:280457/133‑1 (MQ=255)                                                                               ttaGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGa                                              >  1:453645/1‑133 (MQ=255)                                                                                   catcatCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTc                                          >  2:469391/1‑133 (MQ=255)                                                                                        tcCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTaaa                                     >  1:342503/1‑133 (MQ=255)                                                                                             attcattACTTCCGCCTATCAACAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAgg                                <  1:138296/133‑1 (MQ=255)                                                                                             attcattAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAgg                                >  1:433588/1‑133 (MQ=255)                                                                                                   tAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCAtttt                          >  2:474581/1‑133 (MQ=255)                                                                                                   tAATTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCAtttt                          <  1:474581/133‑1 (MQ=255)                                                                                                    aaTTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTc                         <  1:311558/133‑1 (MQ=255)                                                                                                     aTTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        >  1:461192/1‑133 (MQ=255)                                                                                                     aTTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        <  2:476972/133‑1 (MQ=255)                                                                                                     aTTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        <  1:426109/133‑1 (MQ=255)                                                                                                     aTTCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        <  2:342503/133‑1 (MQ=255)                                                                                                       tCCGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAAGTCTGAAGTGAGGCATTTTcaca                      >  1:142449/1‑133 (MQ=255)                                                                                                        ccGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        >  2:5521/1‑130 (MQ=255)                                                                                                        ccGCTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTca                        <  1:5521/130‑1 (MQ=255)                                                                                                           cTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAAt                  >  2:425629/1‑133 (MQ=255)                                                                                                           cTTAACAATAGTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAAt                  >  1:78777/1‑133 (MQ=255)                                                                                                                     gTTTCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAg        >  2:433293/1‑133 (MQ=255)                                                                                                                      tttCACACCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGa       >  1:276841/1‑133 (MQ=255)                                                                                                                        tCACACCTTACCCCCATTGCAACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATa     >  2:10946/1‑133 (MQ=255)                                                                                                                          acacCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCt             >  2:428612/1‑123 (MQ=255)                                                                                                                          acacCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCt             <  1:428612/123‑1 (MQ=255)                                                                                                                          acacCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATaaa   >  2:483543/1‑133 (MQ=255)                                                                                                                           cacCTTACCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATaaaa  >  2:314580/1‑133 (MQ=255)                                                                                                                                 |                                                                                                                               TTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAA  >  NC_000913/2407076‑2407330

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑