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%	229.7 / ‑0.1	73	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 (26/42);  total (27/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

ATTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAGTC  >  NC_000913/532284‑532478                                                                                                 |                                                                                                   aTTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTg                                                                                                 >  2:487938/1‑100 (MQ=255) aTTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTg                                                                                                 >  2:657786/1‑100 (MQ=255)   ttttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGcc                                                                                               <  1:1798531/100‑1 (MQ=255)   ttttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGcc                                                                                               <  2:177838/100‑1 (MQ=255)    tttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCt                                                                                              <  1:1930434/100‑1 (MQ=255)    tttAAATGATAACCCGGTTCAATTTGTGGACTAACTCTAGTTTTGGAAAAATATTACAACTTTCATATTGATGTTATTCTGTTAAGGTTTTAGGTTGACt                                                                                              >  1:220057/1‑100 (MQ=255)     ttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTg                                                                                             <  2:826101/100‑1 (MQ=255)     ttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTg                                                                                             <  1:1765915/100‑1 (MQ=255)     ttACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTg                                                                                             <  1:1874401/100‑1 (MQ=255)       aCATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGtt                                                                                           <  1:1251297/100‑1 (MQ=255)       aCATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGtt                                                                                           >  2:1402122/1‑100 (MQ=255)       aCATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGtt                                                                                           >  2:1402168/1‑100 (MQ=255)         aTGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTan                                                                                         <  2:901341/100‑2 (MQ=255)          tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                        >  2:1225296/1‑100 (MQ=255)          tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                        >  2:805991/1‑100 (MQ=255)          tGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTAtt                                                                                        <  1:679717/100‑1 (MQ=255)           gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                       <  1:336527/100‑1 (MQ=255)           gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                       <  1:1673/100‑1 (MQ=255)           gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                       <  1:1863216/100‑1 (MQ=255)           gATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTg                                                                                       <  2:609627/100‑1 (MQ=255)              aaCCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGaaa                                                                                    <  1:1637333/100‑1 (MQ=255)                cccTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAAcc                                                                                  <  2:804955/100‑1 (MQ=255)                cccTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAAcc                                                                                  >  2:17187/1‑100 (MQ=255)                cccTGTTCAATTTGTGGACTAAATCTAGTTTTCGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAAcc                                                                                  >  1:745892/1‑100 (MQ=255)                   tGTTCAATTTGTGGACTAAATCTAGTTTTTGAAAAATATTCCAACTTTTGTATTGATTTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAg                                                                               <  1:406870/100‑1 (MQ=255)                    gTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGc                                                                              <  1:114968/100‑1 (MQ=255)                     ttCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAg                                                                               <  1:569286/98‑1 (MQ=255)                     ttCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCt                                                                             <  1:805990/100‑1 (MQ=255)                     ttCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCt                                                                             <  1:1225293/100‑1 (MQ=255)                      tCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTg                                                                            <  1:761659/100‑1 (MQ=255)                         aTTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGAcc                                                                         <  2:1629623/100‑1 (MQ=255)                          tttGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCg                                                                        <  2:487083/100‑1 (MQ=255)                                gACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGt                                                                      >  1:1188688/1‑96 (MQ=255)                                gACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggc                                                                  >  2:1323432/1‑100 (MQ=255)                                gACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggc                                                                  >  2:273448/1‑100 (MQ=255)                                 aCTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggcg                                                                 >  1:975958/1‑100 (MQ=255)                                 aCTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTcggcg                                                                 >  1:1328076/1‑100 (MQ=255)                                   tAAATCTAGTTTTGGAAAAATATTTCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggt                                                               <  1:484088/100‑1 (MQ=255)                                   tAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggt                                                               <  1:402374/100‑1 (MQ=255)                                    aaaTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtg                                                              >  2:161435/1‑100 (MQ=255)                                     aaTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtgg                                                             <  2:1510914/100‑1 (MQ=255)                                     aaTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtgg                                                             <  2:1764882/100‑1 (MQ=255)                                      aTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtggt                                                            <  2:1631800/100‑1 (MQ=255)                                      aTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtggt                                                            <  2:962842/100‑1 (MQ=255)                                      aTCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCggtggt                                                            <  2:1100202/100‑1 (MQ=255)                                        cTAGTTTTCGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTGGTTTGCCTGTTATTGAAACCAAGCTGCCCGGTCTGCGGTGGTTg                                                          <  1:794725/100‑1 (MQ=255)                                         tAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGa                                                         >  2:42829/1‑100 (MQ=255)                                            ttttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACg                                                      <  2:1283418/100‑1 (MQ=255)                                            ttttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACg                                                      <  1:345360/100‑1 (MQ=255)                                             tttGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACgg                                                     >  2:1446525/1‑100 (MQ=255)                                                 gAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAAtt                                                 >  1:155040/1‑100 (MQ=255)                                                  aaaaaTATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTa                                                >  2:884375/1‑100 (MQ=255)                                                   aaaaTATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTAt                                               >  2:1820118/1‑100 (MQ=255)                                                        atTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACTGGTCGGCGGTGGTTGAAAGGAATTATGTTAc                                          <  2:1309494/100‑1 (MQ=255)                                                         ttCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACa                                         >  2:1937350/1‑100 (MQ=255)                                                         ttCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACa                                         <  1:1591956/100‑1 (MQ=255)                                                          tCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACaa                                        >  1:1477133/1‑100 (MQ=255)                                                           ccAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAg                                       <  1:931715/100‑1 (MQ=255)                                                            cAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAgg                                      >  1:1052752/1‑100 (MQ=255)                                                                 tttGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACaaa                                 >  1:332006/1‑100 (MQ=255)                                                                   tGTATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACaaaaa                               <  1:732187/100‑1 (MQ=255)                                                                     tATTGATGTTGTTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACacaccga                             >  1:1731056/1‑94 (MQ=255)                                                                      aTTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGAt                            <  1:392402/100‑1 (MQ=255)                                                                           tgttgtTCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAAc                       <  2:1483060/100‑1 (MQ=255)                                                                                ttCTCTTAAGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAg                  >  1:1644769/1‑100 (MQ=255)                                                                                        aGGTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTAcc          <  2:484500/100‑1 (MQ=255)                                                                                         ggTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCg         <  1:17187/100‑1 (MQ=255)                                                                                          gTTTTAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAATGACAAAAAGATGAAACTTCAGGTATTACCGt        >  2:1670421/1‑100 (MQ=255)                                                                                           ttttAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGtt       <  2:827607/100‑1 (MQ=255)                                                                                            tttAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTa      <  2:1636618/100‑1 (MQ=255)                                                                                            tttAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTa      <  2:119803/100‑1 (MQ=255)                                                                                              tAGGTTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGATCGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAg    <  1:1157314/100‑1 (MQ=255)                                                                                                gATTGCTTATTATTGCAACCAAGCTGACCGGTCGGCTGTGGTTGAACGTAATTATGTTACAAGGACAAAAAGATGACACGTCATGTATTACCGTTAAGTc  <  1:1192775/100‑1 (MQ=255)                                                                                                 |                                                                                                   ATTTTTACATGATAACCCTGTTCAATTTGTGGACTAAATCTAGTTTTGGAAAAATATTCCAACTTTTGTATTGATGTTGTTCTCTTAAGGTTTTAGATTGCCTGTTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACGGAATTATGTTACAAGGACAAAAAGATGAAACTTCAGGTATTACCGTTAAGTC  >  NC_000913/532284‑532478

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: ‑