Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	459,642	A→G	18.4%	E252G (GAA→GGA)	lon →	DNA‑binding ATP‑dependent protease La

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	459,642	0	A	G	18.4%	159.9 / 30.3	76	E252G (GAA→GGA)	lon	DNA‑binding ATP‑dependent protease La
Reads supporting (aligned to +/- strand):  ref base A (30/32);  new base G (7/7);  total (37/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CAGATGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCGATG  >  NC_000913/459545‑459739                                                                                                  |                                                                                                  cAGATGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAg                                                                                                 <  2:1341105/100‑1 (MQ=255)  aGATGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGc                                                                                                <  2:502220/100‑1 (MQ=255)    aTGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGccc                                                                                              <  1:1751815/100‑1 (MQ=255)    aTGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGccc                                                                                              <  2:157717/100‑1 (MQ=255)     tGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCt                                                                                             >  1:2294341/1‑100 (MQ=255)     tGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCt                                                                                             <  1:296772/100‑1 (MQ=255)       gagaAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGa                                                                                           <  2:5674/100‑1 (MQ=255)         gaAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAg                                                                                         >  2:214373/1‑100 (MQ=255)         gaAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAg                                                                                         >  2:1609952/1‑100 (MQ=255)         gaAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAg                                                                                         <  1:1263318/100‑1 (MQ=255)         gaAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAg                                                                                         <  1:2040111/100‑1 (MQ=255)          aaaTCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAg                                                                                         <  1:1842915/99‑1 (MQ=255)              cccAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCaa                                                                                    >  2:1840389/1‑100 (MQ=255)               ccAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCaaa                                                                                   >  1:1488890/1‑100 (MQ=255)                       aGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGAcgc                                                                           <  2:609293/100‑1 (MQ=255)                       aGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGAcgc                                                                           >  1:283959/1‑100 (MQ=255)                             aTCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGaa                                                                     >  1:1249728/1‑100 (MQ=255)                             aTCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGaa                                                                     <  2:2065950/100‑1 (MQ=255)                              tCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAg                                                                    <  1:1176772/100‑1 (MQ=255)                              tCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAg                                                                    <  2:1130874/100‑1 (MQ=255)                              tCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAg                                                                    >  1:331057/1‑100 (MQ=255)                               cTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGa                                                                   >  1:2064041/1‑100 (MQ=255)                                tGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGAt                                                                  >  1:1381597/1‑100 (MQ=255)                                tGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGAt                                                                  >  1:1965508/1‑100 (MQ=255)                                  aaCGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGc                                                                <  2:1419771/100‑1 (MQ=255)                                     gAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGa                                                             >  1:1087421/1‑100 (MQ=255)                                      aGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGaa                                                            >  2:5453/1‑100 (MQ=255)                                      aGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGaa                                                            >  1:1433442/1‑100 (MQ=255)                                        cAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGaaa                                                           >  2:702764/1‑99 (MQ=255)                                        cAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAag                                                          <  2:1340427/100‑1 (MQ=255)                                            tGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGc                                                      <  1:2068375/100‑1 (MQ=255)                                             gAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACAAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCa                                                     >  2:1328041/1‑100 (MQ=255)                                               aaGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCaaa                                                   <  1:1781389/100‑1 (MQ=255)                                               aaGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCaaa                                                   <  2:1523077/100‑1 (MQ=255)                                                 gCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAag                                                 <  2:1381583/100‑1 (MQ=255)                                                     ttCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGaa                                             >  2:1157273/1‑100 (MQ=255)                                                     ttCAGAAAGAACTCGGTGAAATGCAAGACGCGCCGGACGAAAACGAAGCACAAAAGCGCAAAATCAACACGGCGAAGACGCCGAAAGAGGCAAAAGAGaa                                             >  2:1467701/1‑100 (MQ=255)                                                       cAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAg                                           <  1:1387479/100‑1 (MQ=255)                                                        agaaagaaCTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGaaa                                            >  1:1312718/1‑98 (MQ=255)                                                           aagaaCTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGa                                       >  2:2239049/1‑100 (MQ=255)                                                              aaCTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGc                                    <  2:1089776/100‑1 (MQ=255)                                                               aCTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGCAAGAGGCAAAAGAGAAAGCGGAAGCa                                   >  1:671720/1‑100 (MQ=255)                                                               aCTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCa                                   >  1:1305906/1‑100 (MQ=255)                                                                cTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCag                                  >  1:950880/1‑100 (MQ=255)                                                                   ggTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCagag                                >  2:1651714/1‑99 (MQ=255)                                                                    gTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGtt                              >  2:1662431/1‑100 (MQ=255)                                                                     tGAAATGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTg                             <  2:2174898/100‑1 (MQ=255)                                                                     tGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTg                             <  2:844386/100‑1 (MQ=255)                                                                      gAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGc                            >  2:2326395/1‑100 (MQ=255)                                                                      gAAATGGACGACGCGCCGGACGAAAACGAAGCCCCGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTg                             <  2:2387222/99‑1 (MQ=255)                                                                        aaTGGACGACGCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAg                          >  2:471249/1‑100 (MQ=255)                                                                        aaTGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGc                            <  1:250194/98‑1 (MQ=255)                                                                         aTGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGa                         >  1:1609834/1‑100 (MQ=255)                                                                            gacgacGCGCGGTACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAAATGCAAAAGAGAAAGCGCAAGTAGAGTTGCAGaa                        <  2:117696/98‑1 (MQ=255)                                                                            gacgacGCGCCGGACGAACACGAAGCCCTAAAGCGCAAAAACGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGc                      <  2:671306/100‑1 (MQ=255)                                                                            gacgacGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGc                      >  2:2358649/1‑100 (MQ=255)                                                                             acgacgCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCt                     <  2:2377384/100‑1 (MQ=255)                                                                             acgacgCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCt                     <  1:2337255/100‑1 (MQ=255)                                                                              cgacgCGCCGGACGAAAACGGAGCCCTGAAGCGCAAAATCGACGCGGCGAATATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCt                     <  2:1975766/99‑1 (MQ=255)                                                                              cgacgCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTg                    >  2:257232/1‑100 (MQ=255)                                                                               gacgCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGa                   <  2:1808217/100‑1 (MQ=255)                                                                               gacgCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGa                   <  2:1249715/100‑1 (MQ=255)                                                                                  gcgcCGGACGAAAACGGAGCCCTGAAGCGCAAAATTGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGaaaa                <  1:659639/100‑1 (MQ=255)                                                                                   cgcCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAat               >  2:1578791/1‑100 (MQ=255)                                                                                    gcCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAATAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAatg              <  2:137442/100‑1 (MQ=255)                                                                                     ccGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAatga             <  1:1359508/100‑1 (MQ=255)                                                                                      cGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAatga             <  2:1450977/99‑1 (MQ=255)                                                                                       ggACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAatgatg           >  1:1730206/1‑100 (MQ=255)                                                                                          cGAAAACGAAGGCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGtct        >  2:1251109/1‑100 (MQ=255)                                                                                          cGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGtct        >  1:2357981/1‑100 (MQ=255)                                                                                          cGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGtct        >  2:807737/1‑100 (MQ=255)                                                                                            aaaaCGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTcc      >  1:1375366/1‑100 (MQ=255)                                                                                             aaaCGAAGCTCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCg     <  1:1873221/100‑1 (MQ=255)                                                                                             aaaCGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCg     <  1:2273761/100‑1 (MQ=255)                                                                                              aaCGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCGa    <  2:2296309/100‑1 (MQ=255)                                                                                                cGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCGATg  >  1:1056713/1‑100 (MQ=255)                                                                                                  |                                                                                                  CAGATGGAGAAATCCCAGCGTGAGTACTATCTGAACGAGCAAATGAAAGCTATTCAGAAAGAACTCGGTGAAATGGACGACGCGCCGGACGAAAACGAAGCCCTGAAGCGCAAAATCGACGCGGCGAAGATGCCGAAAGAGGCAAAAGAGAAAGCGGAAGCAGAGTTGCAGAAGCTGAAAATGATGTCTCCGATG  >  NC_000913/459545‑459739

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑