Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	532,380	A→G	intergenic (‑159/‑71)	allS ← / → allA	allD operon transcriptional activator/ureidoglycolate lyase, releasing urea

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	532,380	0	A	G	94.4%	224.7 / 2.8	72	intergenic (‑159/‑71)	allS/allA	allD operon transcriptional activator/ureidoglycolate lyase, releasing urea
Reads supporting (aligned to +/- strand):  ref base A (1/3);  new base G (29/39);  total (30/42)
Fisher's exact test for biased strand distribution p-value = 6.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01

TTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAG  >  NC_000913/532285‑532476                                                                                                |                                                                                                 tttttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTTGAAAAATATTCTAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTTGGTTg                                                                                               >  2:296535/1‑99 (MQ=255)  ttttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGcc                                                                                             <  1:378902/100‑1 (MQ=255)   tttACATGATAACCCTGTTCAATTTGTGTACTAAATAAAAAAAAAAAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGcc                                                                                             <  2:41302/99‑1 (MQ=255)    ttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTg                                                                                           <  1:622624/100‑1 (MQ=255)       cATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTa                                                                                        >  1:790651/1‑100 (MQ=255)       cATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTa                                                                                        >  2:1347442/1‑100 (MQ=255)       cATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGtt                                                                                         <  1:860161/99‑1 (MQ=255)         tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                      >  1:1076984/1‑100 (MQ=255)         tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                      >  2:1385623/1‑100 (MQ=255)         tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                      >  1:1447578/1‑100 (MQ=255)         tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                      <  2:308222/100‑1 (MQ=255)          gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                     <  2:1202433/100‑1 (MQ=255)          gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                     >  1:538185/1‑100 (MQ=255)          gATAACCCTGTTCAATTTGTGGACTAAATATAAATAAAAAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                     <  2:1476780/100‑1 (MQ=255)             aaCCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGaaa                                                                                  <  1:22529/100‑1 (MQ=255)               cccTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAAcc                                                                                >  1:1259989/1‑100 (MQ=255)                   gTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGc                                                                            <  2:678862/100‑1 (MQ=255)                     tCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTg                                                                          <  2:635932/100‑1 (MQ=255)                      cAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGa                                                                         >  1:741935/1‑100 (MQ=255)                       aaTTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGAc                                                                        <  1:14832/100‑1 (MQ=255)                       aaTTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGAc                                                                        >  2:834340/1‑100 (MQ=255)                        aTTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGAcc                                                                       <  2:1076978/100‑1 (MQ=255)                         tttGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCg                                                                      <  1:1202228/100‑1 (MQ=255)                          ttGTGGACTACATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTGTACGTTGCCTGTTATTGAAACCAAGCTGACCgg                                                                     <  2:1039102/100‑1 (MQ=255)                          ttGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCgg                                                                     <  1:422681/100‑1 (MQ=255)                          ttGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCgg                                                                     <  2:431117/100‑1 (MQ=255)                            gtgGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTc                                                                   >  2:44270/1‑100 (MQ=255)                              ggACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTcgg                                                                 <  1:901344/100‑1 (MQ=255)                               gACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggc                                                                <  1:1473366/100‑1 (MQ=255)                               gACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggc                                                                >  2:133037/1‑100 (MQ=255)                                 cTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggcg                                                               >  1:607812/1‑99 (MQ=255)                                   aaaTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtg                                                            >  2:720956/1‑100 (MQ=255)                                    aaTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtgg                                                           <  2:1573046/100‑1 (MQ=255)                                     aTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtggt                                                          <  1:254470/100‑1 (MQ=255)                                       cTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTg                                                        <  2:1447570/100‑1 (MQ=255)                                        tAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGa                                                       <  1:1147940/100‑1 (MQ=255)                                         aGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGaa                                                      >  2:824120/1‑100 (MQ=255)                                          gTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAAc                                                     <  1:1287196/100‑1 (MQ=255)                                          gTTTTGGAAAAATATTCCAACTTTTGTACTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACTATGCTGACCGGTCGGCGGTGGTTCAAc                                                     >  2:91409/1‑100 (MQ=255)                                           ttttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACg                                                    <  1:438219/100‑1 (MQ=255)                                           ttttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACg                                                    <  1:126622/100‑1 (MQ=255)                                            tttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACgg                                                   >  2:511720/1‑100 (MQ=255)                                            tttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACgg                                                   <  2:373415/100‑1 (MQ=255)                                              tGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGaa                                                 >  2:820517/1‑100 (MQ=255)                                               ggAAAAATATTCCAACTTTTGTATTGATTTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAAt                                                <  2:500597/100‑1 (MQ=255)                                                       atTCCAACTTTTGTATTGATGTTGTTCGCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTAc                                        <  2:261377/100‑1 (MQ=255)                                                          ccAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAg                                     >  1:59121/1‑100 (MQ=255)                                                          ccAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAg                                     <  1:800655/100‑1 (MQ=255)                                                           cAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAgg                                    <  1:1062741/100‑1 (MQ=255)                                                             aCTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTGCAAGGAc                                  <  1:828392/100‑1 (MQ=255)                                                              cTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACa                                 >  2:246792/1‑100 (MQ=255)                                                                 ttGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACaaaa                              <  1:995198/100‑1 (MQ=255)                                                                   gTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAg                            <  2:1159486/100‑1 (MQ=255)                                                                   gTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAg                            <  2:38977/100‑1 (MQ=255)                                                                     aTTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGAt                          <  1:1551615/100‑1 (MQ=255)                                                                     aTTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGAt                          >  2:1460018/1‑100 (MQ=255)                                                                      ttGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATg                         <  1:749445/100‑1 (MQ=255)                                                                      ttGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATg                         >  2:1090512/1‑100 (MQ=255)                                                                       tGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGa                        >  1:842300/1‑100 (MQ=255)                                                                       tGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGa                        <  2:790646/100‑1 (MQ=255)                                                                          tgtggtTCTCTTAAGGTTTTAGGTGTCCTGTTATTGAATCCAAGCTGAGCGGTCGGTGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAAc                     <  2:109838/100‑1 (MQ=255)                                                                            ttgttCTCTTAAGGTTTTAGGTTGCCTGTTCTTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACtt                   >  1:374909/1‑100 (MQ=255)                                                                            ttgttCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACtt                   >  2:1415447/1‑100 (MQ=255)                                                                             tgttCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTc                  >  2:809950/1‑100 (MQ=255)                                                                                tctcTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAgg               >  1:1190256/1‑100 (MQ=255)                                                                                tctcTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAgg               <  2:999170/100‑1 (MQ=255)                                                                                 ctctTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGt              <  1:834345/100‑1 (MQ=255)                                                                                   ctTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTAt            >  2:401784/1‑100 (MQ=255)                                                                                   ctTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTAt            >  1:496088/1‑100 (MQ=255)                                                                                           tttAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTa    <  1:1321210/100‑1 (MQ=255)                                                                                            ttAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTaa   <  1:1385631/100‑1 (MQ=255)                                                                                             tAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAg  >  1:1056439/1‑100 (MQ=255)                                                                                                |                                                                                                 TTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAG  >  NC_000913/532285‑532476

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: ‑