Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,073,764	T→C	N83S (AAC→AGC)	rutA ←	pyrimidine oxygenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,073,764	0	T	C	98.3%	195.9 / ‑4.3	58	N83S (AAC→AGC)	rutA	pyrimidine oxygenase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (26/31);  total (26/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.78e-01

GCCAGAGATGGAGTCGATGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGTTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGCATGTACTGCGGCG  >  NC_000913/1073628‑1073896                                                                                                                                         |                                                                                                                                     gccAGAGATGGAGTCGATGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCtgt                                                                                                                                   <  2:1365476/140‑1 (MQ=255) gccAGAGAGGGAGTCGATGGTTGCGGCCATCCGGGCGACGATTGTCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGTtgt                                                                                                                                   <  2:901165/140‑1 (MQ=255)   caaagaTGGAGTCGATGGTTGCGGCCATACTGGCGACGATTGCCGGAGGTAACTTTAAGGTGGCAGCAGTGGCGTAAATCTGAATTCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGa                                                                                                                                 <  2:873525/137‑1 (MQ=255)   cAGAGATGGAGTCGATGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGa                                                                                                                                 <  2:425429/140‑1 (MQ=255)      agaTGGAGTCGATGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATcc                                                                                                                              <  1:41149/140‑1 (MQ=255)                 aTGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGt                                                                                                                   >  1:774346/1‑140 (MQ=255)                    gTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGtttt                                                                                                                <  1:1063545/140‑1 (MQ=255)                      tGCGGCCATACGGGCGACGATTGCCGGTGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTgc                                                                                                              >  2:182393/1‑140 (MQ=255)                      tGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTgc                                                                                                              >  2:766326/1‑140 (MQ=255)                       gCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGAGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTgcc                                                                                                             >  1:1421137/1‑140 (MQ=255)                        cGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTgccg                                                                                                            >  1:1221531/1‑140 (MQ=255)                             aTACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCaaa                                                                                                       >  2:1423091/1‑140 (MQ=255)                                 gggCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCa                                                                                                   <  1:875093/140‑1 (MQ=255)                                 gggCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCa                                                                                                   <  2:774346/140‑1 (MQ=255)                                 gggCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTAACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCa                                                                                                   <  2:409351/140‑1 (MQ=255)                                  ggCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCAc                                                                                                  <  1:422586/140‑1 (MQ=255)                                    cgacgaTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGc                                                                                                <  1:885417/140‑1 (MQ=255)                                     gacgaTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGc                                                                                                >  1:1222356/1‑139 (MQ=255)                                     gacgaTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGc                                                                                                <  2:1222356/139‑1 (MQ=255)                                      acgaTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAg                                                                                              >  2:654384/1‑140 (MQ=255)                                        gaTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGtt                                                                                            <  1:1287904/140‑1 (MQ=255)                                         aTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAg                                                                                                      >  1:1380307/1‑129 (MQ=255)                                         aTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAg                                                                                                      <  2:1380307/129‑1 (MQ=255)                                         aTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGttt                                                                                           >  1:1305767/1‑140 (MQ=255)                                         aTTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGttt                                                                                           >  2:1264639/1‑140 (MQ=255)                                             ccGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGatc                                                                                       >  1:143456/1‑140 (MQ=255)                                                  ggTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGc                                                                                                <  2:117499/126‑1 (MQ=255)                                                  ggTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGc                                                                                                >  1:117499/1‑126 (MQ=255)                                                   gTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGAc                                                                                 <  2:53121/140‑1 (MQ=255)                                                             ggTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGcgaaat                                                                       <  1:766326/140‑1 (MQ=255)                                                             ggTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGcgaaat                                                                       <  1:1264639/140‑1 (MQ=255)                                                             ggTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGcgaaat                                                                       <  1:292594/140‑1 (MQ=255)                                                             ggTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGcgaaat                                                                       <  2:1305767/140‑1 (MQ=255)                                                                 gcagcaGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGcgaaatcgaa                                                                   >  2:1210424/1‑140 (MQ=255)                                                                 gcagcaGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCAACGCAGTTTGATCATCGACAGGGcgaaatcgaa                                                                   >  1:933663/1‑140 (MQ=255)                                                                     cagTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATgg                                                               <  1:654384/140‑1 (MQ=255)                                                                     cagTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATgg                                                               <  1:227293/140‑1 (MQ=255)                                                                         ggCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGt                                                           >  1:1395804/1‑140 (MQ=255)                                                                               aaTCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCg                                                     >  1:295689/1‑140 (MQ=255)                                                                                 tCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCt                                                   <  1:1319405/140‑1 (MQ=255)                                                                                    gAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCtttt                                                >  2:297429/1‑140 (MQ=255)                                                                                     aaTGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCttttt                                               >  2:1423286/1‑140 (MQ=255)                                                                                          gcgAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGcaca                                          >  1:568000/1‑140 (MQ=255)                                                                                           cgAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACaa                                         <  2:1221531/140‑1 (MQ=255)                                                                                           cgAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACaa                                         <  1:907601/140‑1 (MQ=255)                                                                                           cgAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACaa                                         <  1:1423286/140‑1 (MQ=255)                                                                                           cgAGGTCACGGCCACCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACaa                                         <  1:597034/140‑1 (MQ=255)                                                                                            gAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAAt                                        >  1:229229/1‑140 (MQ=255)                                                                                                   cGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTa                                 >  2:294390/1‑140 (MQ=255)                                                                                                     gccgccAGCCCCGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTAtt                               <  2:568000/140‑1 (MQ=255)                                                                                                              cccGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCaaa                      <  1:394082/140‑1 (MQ=255)                                                                                                                cGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAgg                    <  2:143456/140‑1 (MQ=255)                                                                                                                cGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAgg                    <  1:102371/140‑1 (MQ=255)                                                                                                                cGCCATCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAgg                    >  1:1418094/1‑140 (MQ=255)                                                                                                                     tCAAGGTGAACGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGc               <  1:297429/140‑1 (MQ=255)                                                                                                                             aaCGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCGGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGCATGTACTg       >  2:1242375/1‑140 (MQ=255)                                                                                                                             aaCGACTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGCATGTACTg       >  1:630196/1‑140 (MQ=255)                                                                                                                                  cTCAAGGCTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGCATGTACTgcggcg  >  1:332156/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                     GCCAGAGATGGAGTCGATGGTTGCGGCCATACGGGCGACGATTGCCGGAGGTAACGTTAAGGTGGCAGCAGTGGCGTAAATCTGAATGCGCGAGGTCACGGCCGCCAGCCCCGCCATCAAGGTGAACGACTCAAGGTTGTGATCCCAGAACTCAGTTTTGCCGCCAAAGCCACGCAGTTTGATCATCGACAGGGCGAAATCGAAATGGTAGTGCTCCGCTTTTTGCACAATGGCTTTATTCAGTTCAAAGGTCGGCATGTACTGCGGCG  >  NC_000913/1073628‑1073896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑