Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	874,056	G→A	17.3%	E360K (GAA→AAA)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	874,056	0	G	A	17.3%	161.7 / 22.9	75	E360K (GAA→AAA)	yliE	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base G (28/33);  new base A (8/5);  total (36/39)
Fisher's exact test for biased strand distribution p-value = 3.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.82e-01

CCTGACTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACAATAATCAG  >  NC_000913/873957‑874154                                                                                                    |                                                                                                   ccTGACTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCg                                                                                                    >  2:852058/1‑100 (MQ=255)  cTGACTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCAATCGAGGAAATGAAAGATGCCGa                                                                                                   >  1:821795/1‑100 (MQ=255)   tGACTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGaa                                                                                                  >  2:515692/1‑100 (MQ=255)      cTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGaaa                                                                                                 >  1:94389/1‑98 (MQ=255)      cTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAAtt                                                                                               >  2:1811989/1‑100 (MQ=255)        cAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGa                                                                                             <  2:1762624/100‑1 (MQ=255)         aaCGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGaa                                                                                            >  1:650981/1‑100 (MQ=255)          aCGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAAc                                                                                           <  1:249938/100‑1 (MQ=255)             gATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACgg                                                                                         >  2:965062/1‑99 (MQ=255)                 aaaTCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCaaa                                                                                    >  1:1759095/1‑100 (MQ=255)                      gAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCaaataaat                                                                               <  1:2068689/100‑1 (MQ=255)                         gCTCTGAAAATTCGTGAAGGCGATGTGAAAGAAATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTCAACGGTCAAATAAATTGc                                                                            <  2:754131/100‑1 (MQ=255)                         gCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGc                                                                            <  1:206830/100‑1 (MQ=255)                          ctctGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGct                                                                           >  1:2178772/1‑100 (MQ=255)                           tctGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGctc                                                                          <  2:74938/100‑1 (MQ=255)                           tctGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGctc                                                                          >  2:1776286/1‑100 (MQ=255)                             taaaaaTTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGctctn                                                                        <  1:1997623/98‑2 (MQ=255)                             tGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCtctc                                                                        >  1:1011528/1‑100 (MQ=255)                             tGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCtctc                                                                        >  1:415782/1‑100 (MQ=255)                             tGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGCtctc                                                                        >  1:1282353/1‑100 (MQ=255)                               aaaaTTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCAc                                                                      <  2:343548/100‑1 (MQ=255)                                aaaTTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACt                                                                     <  1:388794/100‑1 (MQ=255)                                   ttCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGAt                                                                  >  2:1767156/1‑100 (MQ=255)                                      gTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGAtc                                                                 <  1:2169961/98‑1 (MQ=255)                                        gAAGGCGATTCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCtt                                                             <  1:561984/100‑1 (MQ=255)                                         acggCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTa                                                            <  2:1048069/98‑1 (MQ=255)                                         aaGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCTGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCGTa                                                            <  2:2039715/100‑1 (MQ=255)                                          aGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTAc                                                           <  1:1024779/100‑1 (MQ=255)                                          aGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTAc                                                           <  2:1086170/100‑1 (MQ=255)                                           ggCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACg                                                          <  2:1759074/100‑1 (MQ=255)                                             cGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGAt                                                        >  1:1016460/1‑100 (MQ=255)                                              gATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATc                                                       >  1:1790784/1‑100 (MQ=255)                                              gATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATc                                                       <  1:1496117/100‑1 (MQ=255)                                                 gCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAgg                                                    >  2:1651219/1‑100 (MQ=255)                                                  cGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGa                                                   >  1:1473574/1‑100 (MQ=255)                                                  cGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGa                                                   >  2:2356531/1‑100 (MQ=255)                                                   gAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGaa                                                  >  1:326403/1‑100 (MQ=255)                                                    aaaGAGATTATCATCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGaaa                                                 <  1:2246669/100‑1 (MQ=255)                                                     aaGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAg                                                >  2:347173/1‑100 (MQ=255)                                                     aaGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGATCAAATAAATTGCTCTCGCTGATCTCTTACGATCACAAAAg                                                >  2:2385064/1‑100 (MQ=255)                                                     aaGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCAAAAATTGAACGGGCAAATAAATAGCTCTCACTAATCTCGTACGATCAAGAAAg                                                >  2:1043921/1‑100 (MQ=255)                                                       gagaTTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTg                                              <  1:1497121/100‑1 (MQ=255)                                                       gagaTTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTg                                              >  1:2182967/1‑100 (MQ=255)                                                       gagaTTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTg                                              >  1:2115250/1‑100 (MQ=255)                                                              tCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTttat                                       >  1:2295373/1‑100 (MQ=255)                                                                aGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTAAACGGTCAAATAAATTGCTCTCACTGATCTCTTACAATCAGGAAAGTGGTTttatta                                     >  2:630672/1‑100 (MQ=255)                                                                 gCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTaa                                    <  2:1473558/100‑1 (MQ=255)                                                                 gCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCACACTGATCTCTTACGATCAGGAAAGTGGTTTTATTaa                                    >  2:1612841/1‑100 (MQ=255)                                                                   aTCAAAAATTCGATGGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTaaaa                                  <  2:1632036/100‑1 (MQ=255)                                                                   aTCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTaaaa                                  <  1:946698/100‑1 (MQ=255)                                                                   aTCAAAAATTCGATCGCAGAAATGAAAAATGGCAAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGAACAGGAAAGTCGTTTTATTaaaa                                  >  2:517803/1‑100 (MQ=255)                                                                      aaaaaTTCGATCACAGAAACGAAAGATGCCGAAATAGAACCTTCAAATAAATTGCTCTCGCTGATCTCTTCCGCTCAGCAAAGTGGTTTTATAACAAata                               >  2:297312/1‑100 (MQ=255)                                                                       aaaaTTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAata                               <  1:824237/99‑1 (MQ=255)                                                                        aaaTTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATg                             <  1:314886/100‑1 (MQ=255)                                                                         aaTTCGATCGCGGAAATGAAAGATGCCCAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGTTTAGGAAAGTTGTTTTATTAAAAATATgg                            <  2:1362967/100‑1 (MQ=255)                                                                              gATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGatt                       >  1:723125/1‑100 (MQ=255)                                                                                  gcgGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGattatt                    <  1:623349/99‑1 (MQ=255)                                                                                   cgGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTg                   <  1:1279664/99‑1 (MQ=255)                                                                                   cgGAAATGAAAGATGCCAAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGa                  >  1:965703/1‑100 (MQ=255)                                                                                    ggAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAg                 <  1:2141821/100‑1 (MQ=255)                                                                                    ggAAAGGAATGATGTAGAAATGGAACGGTGAAATAAATTGCTCTTACTGATCAATTATTATAAGGAAAGTGGTTTTATTAAAATTAGGGAGGTAATTGAg                 <  2:467105/100‑1 (MQ=255)                                                                                      aaaTGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATAGCGATTATTGa                  >  1:820083/1‑97 (MQ=255)                                                                                      aaaTGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTCATTAAAAATATGGCGATTATTGAGTc               <  1:1458700/100‑1 (MQ=255)                                                                                      aaaTGAAAGATGCCAAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTc               <  2:359354/100‑1 (MQ=255)                                                                                         tGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCt              <  2:694400/98‑1 (MQ=255)                                                                                         tGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTaa            >  1:888280/1‑100 (MQ=255)                                                                                          gAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAAc           <  2:2015297/100‑1 (MQ=255)                                                                                          gAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAAc           <  2:818474/100‑1 (MQ=255)                                                                                          gAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAAc           <  2:816708/100‑1 (MQ=255)                                                                                            aaGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACaa         >  1:1179233/1‑100 (MQ=255)                                                                                             aGATGGCGAAATTGAACGGTCAAATAAATTGCTCTCACTGAACTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACaat        <  1:1122410/100‑1 (MQ=255)                                                                                             aGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACaat        <  1:1937968/100‑1 (MQ=255)                                                                                               aTGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGGGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACaataa      >  2:1447053/1‑100 (MQ=255)                                                                                                tGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACaataat     <  2:899898/100‑1 (MQ=255)                                                                                                 gCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACAATAATc    <  2:1358311/100‑1 (MQ=255)                                                                                                   cGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACAATAATCAg  >  1:2008966/1‑100 (MQ=255)                                                                                                    |                                                                                                   CCTGACTCAACGGATCAAATCGAGGCTCTGAAAATTCGTGAAGGCGATGCGAAAGAGATTATCAGCATCAAAAATTCGATCGCGGAAATGAAAGATGCCGAAATTGAACGGTCAAATAAATTGCTCTCACTGATCTCTTACGATCAGGAAAGTGGTTTTATTAAAAATATGGCGATTATTGAGTCTAACAATAATCAG  >  NC_000913/873957‑874154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑