Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	189,045	A→T	E235V (GAA→GTA)	pyrH →	UMP kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	189,045	0	A	T	93.0%	188.0 / 6.2	57	E235V (GAA→GTA)	pyrH	UMP kinase
Reads supporting (aligned to +/- strand):  ref base A (2/2);  new base T (29/24);  total (31/26)
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

AGCGAAGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCGCAG  >  NZ_CP009273/188909‑189176                                                                                                                                         |                                                                                                                                    aGCGAAGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAaagtag                                                                                                                                   <  2:130684/139‑1 (MQ=255)     aaGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGAc                                                                                                                               >  1:1074949/1‑139 (MQ=255)     aaGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGAc                                                                                                                               >  1:1227693/1‑139 (MQ=255)     aaGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGAc                                                                                                                               >  1:865704/1‑139 (MQ=255)                  agagCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGaa                                                                                                                  >  2:818582/1‑139 (MQ=255)                             tCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       <  2:917772/139‑1 (MQ=255)                               aTGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGAt                                                                                                     <  2:865704/139‑1 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       >  1:1075407/1‑129 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       <  2:1075407/129‑1 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaa                                                                                              >  2:711942/1‑138 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaa                                                                                              >  2:805005/1‑138 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       <  1:476099/129‑1 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       >  2:476099/1‑129 (MQ=255)                                       ggcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGAAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaa                                                                                              >  1:1242562/1‑138 (MQ=255)                                        gcggcCTTCCCGCTGGTTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaat                                                                                             <  2:157960/138‑1 (MQ=255)                                        gcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaat                                                                                             >  1:436190/1‑138 (MQ=255)                                        gcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaat                                                                                             <  2:85583/138‑1 (MQ=255)                                        gcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaat                                                                                             <  2:328007/138‑1 (MQ=255)                                        gcggcCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaat                                                                                             <  1:805005/138‑1 (MQ=255)                                                     tGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTcc                                                                               >  1:525789/1‑139 (MQ=255)                                                       gCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCcgc                                                                             <  1:818582/139‑1 (MQ=255)                                                           gTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGt                                                                           <  2:672960/137‑1 (MQ=255)                                                            tGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAg                                                                        <  2:436190/139‑1 (MQ=255)                                                                 aTAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATcg                                                                   >  2:469530/1‑139 (MQ=255)                                                                    aaTTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCgg                                                                <  2:826900/139‑1 (MQ=255)                                                                    aaTTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGAC‑TTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCgg                                                                <  1:754376/138‑1 (MQ=255)                                                                       tACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaataa                                                                                           <  1:16636/109‑1 (MQ=255)                                                                       tACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGataaataa                                                                                           >  2:16636/1‑109 (MQ=255)                                                                         ccGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCg                                                           >  1:21876/1‑139 (MQ=255)                                                                             ttCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAg                                                       >  1:1243570/1‑139 (MQ=255)                                                                                gtgtTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTc                                                     <  2:1289142/138‑1 (MQ=255)                                                                                gtgtTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTc                                                     <  2:21876/138‑1 (MQ=255)                                                                                gtgtTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCt                                                    >  2:1130802/1‑139 (MQ=255)                                                                                          tatGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAgg                                          <  2:1227693/139‑1 (MQ=255)                                                                                              aaCAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGt                                       <  2:1287482/138‑1 (MQ=255)                                                                                                 aaaCCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTAtt                                   <  2:690106/139‑1 (MQ=255)                                                                                                        gTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTgcag                            >  1:1277197/1‑139 (MQ=255)                                                                                                        gTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTgcag                            >  2:137446/1‑139 (MQ=255)                                                                                                         tgcgctgcgcCGTGTGGTAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTgcagg                           <  2:1074949/139‑1 (MQ=255)                                                                                                                          tAATGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGc            >  2:1008289/1‑137 (MQ=255)                                                                                                                            aTGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTc                 >  2:734101/1‑130 (MQ=255)                                                                                                                            aTGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTc                 <  1:734101/130‑1 (MQ=255)                                                                                                                             tGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGtt                      >  1:250125/1‑124 (MQ=255)                                                                                                                             tGGGTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGtt                      <  2:250125/124‑1 (MQ=255)                                                                                                                               ggTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       >  2:769608/1‑41 (MQ=255)                                                                                                                               ggTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTg                                                                                                       <  1:769608/41‑1 (MQ=255)                                                                                                                               ggTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcg     >  2:1278464/1‑139 (MQ=255)                                                                                                                               ggTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcg     >  2:1035562/1‑139 (MQ=255)                                                                                                                               ggTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcg     >  1:523530/1‑139 (MQ=255)                                                                                                                               ggTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcg     >  2:395727/1‑139 (MQ=255)                                                                                                                               ggTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgc      <  1:816997/138‑1 (MQ=255)                                                                                                                                gTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcgc    <  1:137446/139‑1 (MQ=255)                                                                                                                                gTGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcgc    <  1:1130802/139‑1 (MQ=255)                                                                                                                                 tGAAAAAGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAgcgcg     >  2:1141480/1‑137 (MQ=255)                                                                                                                                   aaaaaGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCgcag  >  2:254001/1‑138 (MQ=255)                                                                                                                                   aaaaaGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCgcag  >  2:505304/1‑138 (MQ=255)                                                                                                                                   aaaaaGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCgcag  >  1:848667/1‑138 (MQ=255)                                                                                                                                   aaaaaGTAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCgcag  >  1:344656/1‑138 (MQ=255)                                                                                                                                         |                                                                                                                                    AGCGAAGTGCTGGAAAAAGAGCTGAAAGTCATGGACCTGGCGGCCTTCACGCTGGCTCGTGACCATAAATTACCGATTCGTGTTTTCAATATGAACAAACCGGGTGCGCTGCGCCGTGTGGTAATGGGTGAAAAAGAAGGGACTTTAATCACGGAATAATTCCCGTGATGGATAAATAAGGGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGTTATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCGCAG  >  NZ_CP009273/188909‑189176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑