Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,576,651	T→C	I85T (ATT→ACT)	BW25113_RS17825 →	YrhA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,576,651	0	T	C	93.3%	192.2 / 4.5	60	I85T (ATT→ACT)	BW25113_RS17825	YrhA family protein
Reads supporting (aligned to +/- strand):  ref base T (3/1);  new base C (28/28);  total (31/29)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.84e-02

ATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATT  >  NZ_CP009273/3576519‑3576784                                                                                                                                     |                                                                                                                                      attcAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCa                                                                                                                                   <  2:320534/137‑1 (MQ=255) attcAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAg                                                                                                                                  >  2:124085/1‑138 (MQ=255)         aaTTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAATCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAg                                                                                                                         >  1:857559/1‑139 (MQ=255)                 ggAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAAc                                                                                                                 >  2:839210/1‑139 (MQ=255)                 ggAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAAc                                                                                                                 >  1:933893/1‑139 (MQ=255)                  gagaAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAAcc                                                                                                                >  1:704026/1‑139 (MQ=255)                  gagaAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAAcc                                                                                                                >  2:430549/1‑139 (MQ=255)                        ttATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTg                                                                                                          >  1:1051560/1‑139 (MQ=255)                        ttATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTc                                                                                                                           <  2:150345/122‑1 (MQ=255)                        ttATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTc                                                                                                                           >  1:150345/1‑122 (MQ=255)                        ttATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTg                                                                                                          >  1:1221479/1‑139 (MQ=255)                             tAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGt                                                                                                      >  2:631261/1‑138 (MQ=255)                                tGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAAt                                                                                                  <  1:391235/139‑1 (MQ=255)                                  aaGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATg                                                                                                 >  1:162389/1‑138 (MQ=255)                                  aaGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATg                                                                                                 >  1:447816/1‑138 (MQ=255)                                     ttAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAAt                                                                                                  <  2:378130/134‑1 (MQ=255)                                     ttAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAAt                                                                                                  >  1:378130/1‑134 (MQ=255)                                       aGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAAttt                                                                                            >  2:986847/1‑138 (MQ=255)                                        gTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTta                                                                                          <  2:1051560/139‑1 (MQ=255)                                         tATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTtat                                                                                         <  1:190477/139‑1 (MQ=255)                                         tATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTtat                                                                                         <  1:986847/139‑1 (MQ=255)                                              tttttAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGaaa                                                                                    >  1:1025532/1‑139 (MQ=255)                                                  tAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAaataat                                                                                >  2:223663/1‑139 (MQ=255)                                                                aTTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATaaa                                                                  >  2:31441/1‑139 (MQ=255)                                                                   aTCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAcc                                                                <  2:162389/138‑1 (MQ=255)                                                                   aTCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAcc                                                                <  1:655049/138‑1 (MQ=255)                                                                    tCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               <  2:447816/138‑1 (MQ=255)                                                                    tCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               <  2:17804/138‑1 (MQ=255)                                                                        aCTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTg                                                             <  2:686309/136‑1 (MQ=255)                                                                              ttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAc                                                       >  1:1136600/1‑136 (MQ=255)                                                                              ttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAc                                                       >  1:150350/1‑136 (MQ=255)                                                                              ttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAc                                                       >  2:370437/1‑136 (MQ=255)                                                                               tAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAg                                                    <  1:631261/138‑1 (MQ=255)                                                                                 agagCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGaa                                                  <  2:933893/138‑1 (MQ=255)                                                                                      aaTGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGt                                              >  2:343229/1‑137 (MQ=255)                                                                                      aaTGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTa                                            <  1:31441/139‑1 (MQ=255)                                                                                        tggatggaTTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGt                                          <  1:660588/139‑1 (MQ=255)                                                                                            tggatTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATc                                      <  2:1221479/139‑1 (MQ=255)                                                                                              gatTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGGCTCCAGAACCTTCAGTTAAAATCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAGCCCTGATCTACAAGAACGGTTAGTGATCg                                     <  2:1263108/138‑1 (MQ=255)                                                                                              gatTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCg                                     <  1:839210/138‑1 (MQ=255)                                                                                               atTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               >  2:614172/1‑111 (MQ=255)                                                                                               atTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               <  1:614172/111‑1 (MQ=255)                                                                                                    aaGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATta                              >  1:105961/1‑139 (MQ=255)                                                                                                         aaTGGATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCa                         >  1:723446/1‑139 (MQ=255)                                                                                                             gATTACGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCAttt                      <  1:493181/138‑1 (MQ=255)                                                                                                                 aCGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               <  2:46124/93‑1 (MQ=255)                                                                                                                 aCGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAccc                                                               >  1:46124/1‑93 (MQ=255)                                                                                                                 aCGATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAg                                                    >  1:536275/1‑104 (MQ=255)                                                                                                                 aCGATTATTTAGCCTCACGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAg                                                    <  2:536275/104‑1 (MQ=255)                                                                                                                   gATTATTTAGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATAtt               <  2:828838/139‑1 (MQ=255)                                                                                                                           aGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTAt        <  2:704026/138‑1 (MQ=255)                                                                                                                           aGCCTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTACAATATTTACTTAt        <  1:433878/138‑1 (MQ=255)                                                                                                                             ccTCTCGACTCCAGAACCTTCTGTTAAAAACCTTTTTGCCGTAAATGATTTTTATAGAACTAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATc                                      >  2:612866/1‑106 (MQ=255)                                                                                                                             ccTCTCGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATc                                      <  1:612866/106‑1 (MQ=255)                                                                                                                                 tcGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACa                                                      <  1:153018/86‑1 (MQ=255)                                                                                                                                 tcGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACa                                                      >  2:153018/1‑86 (MQ=255)                                                                                                                                 tcGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACAtt  >  1:274762/1‑138 (MQ=255)                                                                                                                                 tcGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACAtt  >  2:1142928/1‑138 (MQ=255)                                                                                                                                  cGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTtat                                                                                         >  1:1126060/1‑50 (MQ=255)                                                                                                                                  cGACTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTtat                                                                                         <  2:1126060/50‑1 (MQ=255)                                                                                                                                     |                                                                                                                                      ATTCAACTAATTGCCTGGAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATT  >  NZ_CP009273/3576519‑3576784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑