Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	607,884	G→A	19.1%	R209* (CGA→TGA)	USA300HOU_0550 ←	deoxynucleoside kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	607,884	0	G	A	19.1%	113.2 / 19.2	57	R209* (CGA→TGA)	USA300HOU_0550	deoxynucleoside kinase
Reads supporting (aligned to +/- strand):  ref base G (22/23);  new base A (7/4);  total (29/28)
Fisher's exact test for biased strand distribution p-value = 5.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01

GTATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGTAT  >  CP000730/607746‑608023                                                                                                                                           |                                                                                                                                            gtATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAg                                                                                                                                           <  1:551110/141‑1 (MQ=255)   atatGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCa                                                                                                                                         <  1:119433/141‑1 (MQ=255)      tgtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                                      <  2:468912/141‑1 (MQ=255)      tgtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                                      <  2:468921/141‑1 (MQ=255)             tAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTa                                                                                                                               <  1:116407/141‑1 (MQ=255)                tGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCa                                                                                                                            >  2:21887/1‑141 (MQ=255)                tGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCa                                                                                                                            >  2:82507/1‑141 (MQ=255)                        acaGAACTGATTAAGTAATCCATAATATCTACGCAATATACATTGAATATAAACACATACGCTATGTCTTTAGTCTTTCATTGCTTAGCTACTGTTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGAttt                                                                                                                    <  2:473248/139‑1 (MQ=255)                          aGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTaa                                                                                                                  <  1:12291/141‑1 (MQ=255)                          aGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTaa                                                                                                                  >  2:450775/1‑141 (MQ=255)                            aaTTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTTAATAATTAAAGTAATTGTGTGTATTATAGGATTTAAAg                                                                                                                >  2:552603/1‑141 (MQ=255)                             aTTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGGTTTGAAGa                                                                                                               >  1:78597/1‑141 (MQ=255)                                   aaaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATAGGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCggg                                                                                                         >  1:584946/1‑141 (MQ=255)                                     aataatCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGt                                                                                                       <  1:313457/141‑1 (MQ=255)                                                  atCTATGGAATATACATAGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATATGATTTAAAGATTCGGGGGCCTTATGGATATc                                                                                          >  2:428276/1‑141 (MQ=255)                                                    cTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCat                                                                                        >  1:418288/1‑141 (MQ=255)                                                      aTGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCatat                                                                                      <  1:581626/141‑1 (MQ=255)                                                        ggAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTc                                                                                    <  2:239363/141‑1 (MQ=255)                                                              taCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATGTCATATTCATTAat                                                                              >  2:594469/1‑141 (MQ=255)                                                                     aaTATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATa                                                                       >  1:311972/1‑141 (MQ=255)                                                                       tataAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                                     <  2:295613/141‑1 (MQ=255)                                                                       tataAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                                     <  1:144424/141‑1 (MQ=255)                                                                           aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACa                                                                 >  1:349405/1‑141 (MQ=255)                                                                           aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACa                                                                 <  1:239277/141‑1 (MQ=255)                                                                             cATTTACGATATGTCTTTTGTATTTCTTCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAAc                                                               <  2:610816/141‑1 (MQ=255)                                                                              atatACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACt                                                              >  1:68349/1‑141 (MQ=255)                                                                               tataCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTg                                                             >  1:201971/1‑141 (MQ=255)                                                                                ataCGCTATGTCTTTAGTCTTTTATCGTGTATCTAGTTGTCGATATGTTTGAATAATTAGAGCGATTTTGTTTATCATAGGTTTTAAAGATTCGGGGTCCTTATGAATATCATATTCATTCATATTTATACGTACAACTgg                                                            >  2:245842/1‑141 (MQ=255)                                                                                   cGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGTTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACa                                                         <  2:394479/141‑1 (MQ=255)                                                                                   cGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACa                                                         <  2:536196/141‑1 (MQ=255)                                                                                   cGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACa                                                         <  1:318926/141‑1 (MQ=255)                                                                                   agatatgtatgTAGGCTTTTATTGTGTAACTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACa                                                         <  1:440718/138‑1 (MQ=255)                                                                                     cTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATg                                                       <  1:450775/141‑1 (MQ=255)                                                                                     cTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAAATGTACAtc                                                       >  2:320881/1‑140 (MQ=255)                                                                                       aTGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCa                                                     >  1:568668/1‑141 (MQ=255)                                                                                       aTGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCa                                                     >  1:260433/1‑141 (MQ=255)                                                                                        tGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAt                                                    <  1:106666/141‑1 (MQ=255)                                                                                         gtctttagtctttaATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTGGTGTATCATAGGATGTAAAGATTCGGGGACATCATGGATATCATATTCATTAATATTGATACGTACATCTGGACGTGCAtt                                                   >  2:590083/1‑141 (MQ=255)                                                                                            tttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTaaa                                                <  1:328935/141‑1 (MQ=255)                                                                                             ttATTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                               <  2:506061/141‑1 (MQ=255)                                                                                                  cTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTATAGCTAtt                                          >  1:392220/1‑141 (MQ=255)                                                                                                           tgtATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATc                                 >  2:147444/1‑141 (MQ=255)                                                                                                           ggtATCTACTTGTGGAGATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATc                                 <  1:186041/140‑1 (MQ=255)                                                                                                            gtATCTACTTGTCGATTTGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCg                                >  1:303484/1‑141 (MQ=255)                                                                                                             tATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                               <  2:68349/141‑1 (MQ=255)                                                                                                                       tCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGCCATAGCGttt                     >  2:95765/1‑141 (MQ=255)                                                                                                                           tatGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAAt                 <  2:418288/141‑1 (MQ=255)                                                                                                                             ggTTTGAATAACTGCAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAg               <  1:86598/140‑1 (MQ=255)                                                                                                                                  gAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTCAATAGCtttt          >  1:40675/1‑141 (MQ=255)                                                                                                                                   aataatTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGGTATCATATTCATTAATATTGATACGTACAACTGGAGATGCATTCAAGCTATTAATCCAATCGTCATAGTGTTTAAATAGCttttt         >  2:267907/1‑141 (MQ=255)                                                                                                                                    ataatTCGAGCAATTTTGTTTATCACAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCttttac        <  2:309448/141‑3 (MQ=255)                                                                                                                                       atTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAGTTGCTTTTTCCAg     >  2:20458/1‑141 (MQ=255)                                                                                                                                        ttCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCatt    >  1:141842/1‑139 (MQ=255)                                                                                                                                        ttCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGt    >  1:71343/1‑141 (MQ=255)                                                                                                                                        ttCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGt    >  1:524394/1‑141 (MQ=255)                                                                                                                                         tCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAGTCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGTa   >  2:269364/1‑141 (MQ=255)                                                                                                                                          cGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGTAt  <  2:307888/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                            GTATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAGTAT  >  CP000730/607746‑608023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑