Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,454,883	A→G	7.0%	I226I (ATT→ATC)	arlS ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,454,883	0	A	G	7.0%	161.5 / 4.1	57	I226I (ATT→ATC)	arlS	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (31/22);  new base G (2/2);  total (33/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.46e-01

AACGATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAGTA  >  CP000730/1454743‑1455021                                                                                                                                             |                                                                                                                                           aaCGATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCa                                                                                                                                            <  1:435332/141‑1 (MQ=255)    gATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAAtt                                                                                                                                         <  1:167407/141‑1 (MQ=255)    gATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAAtt                                                                                                                                         <  1:396638/141‑1 (MQ=255)    gATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAAtt                                                                                                                                         <  1:167383/141‑1 (MQ=255)       tcttctAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTgg                                                                                                                                      <  1:291150/141‑1 (MQ=255)        cttctAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGc                                                                                                                                     >  2:618551/1‑141 (MQ=255)        cttctAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGc                                                                                                                                     <  1:221444/141‑1 (MQ=255)         ttctAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACCAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCt                                                                                                                                    >  1:650509/1‑141 (MQ=255)           ctAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTACATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCtca                                                                                                                                  <  1:422132/141‑1 (MQ=255)             aaTACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCtcatc                                                                                                                                >  1:601946/1‑141 (MQ=255)                aCTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCatcatc                                                                                                                             >  1:673453/1‑141 (MQ=255)                      gggTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTa                                                                                                                       <  1:563722/141‑1 (MQ=255)                         tCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAGTTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAAc                                                                                                                    >  1:327160/1‑141 (MQ=255)                             tttttCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACATATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTAt                                                                                                                >  2:388195/1‑141 (MQ=255)                                  ccccATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCt                                                                                                           <  1:618551/141‑1 (MQ=255)                                    ccATCGCTGAATAAAATTTAAATGACCTTGTATAATTTGTAATGGTGTTAGTAATTCATGTGACGCGTCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGGTGATGATATTATTAAAAGGATTTGCTaa                                                                                                         >  2:406134/1‑141 (MQ=255)                                         gCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTAt                                                                                                    >  1:113628/1‑141 (MQ=255)                                          cTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATc                                                                                                   >  1:152504/1‑141 (MQ=255)                                               tCAAATTTAAATGACCTCGAATAATTTGTAATGGGGTTCGTAATTCATGTGACGCATCTTCCACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTTGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTAttt                                                                                              >  1:579076/1‑141 (MQ=255)                                                          tGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAAttt                                                                                   <  1:216343/141‑1 (MQ=255)                                                           gACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTg                                                                                  >  1:437008/1‑141 (MQ=255)                                                             ccTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTa                                                                                >  2:565149/1‑141 (MQ=255)                                                             ccTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTa                                                                                >  2:382989/1‑141 (MQ=255)                                                             ccTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTa                                                                                >  2:156113/1‑141 (MQ=255)                                                                 gAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTa                                                                            >  1:574949/1‑141 (MQ=255)                                                                      atTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGc                                                                       <  1:380019/141‑1 (MQ=255)                                                                         tGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTACTTGCAat                                                                    >  1:111602/1‑141 (MQ=255)                                                                          gTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAatt                                                                   >  1:52035/1‑141 (MQ=255)                                                                           tAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAattt                                                                  >  2:725665/1‑141 (MQ=255)                                                                           tAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAattt                                                                  >  2:725570/1‑141 (MQ=255)                                                                                   ttCGTAATTCATGTGACGCACCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGaa                                                          <  2:326737/141‑1 (MQ=255)                                                                                     tgTAATTCATGTCACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCAT‑AAATCATTAAACGTATTTGCTATATTATCTATTTCTACATAATTTGTATTTAATTGCTATTTATTTTGAGAAc                                                       <  2:174293/140‑1 (MQ=255)                                                                                     cGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGaaaa                                                        <  1:579316/141‑1 (MQ=255)                                                                                           tCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCAtct                                                  <  1:265020/141‑1 (MQ=255)                                                                                            cATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCAtctc                                                 >  2:10863/1‑141 (MQ=255)                                                                                                     cATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAAtct                                        <  1:278429/141‑1 (MQ=255)                                                                                                             acaaATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCAtt                                <  2:4422/141‑1 (MQ=255)                                                                                                             acaaATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCAtt                                >  2:105297/1‑141 (MQ=255)                                                                                                              caaATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCAttt                               <  2:269248/141‑1 (MQ=255)                                                                                                                 aTTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTAt                            >  1:346294/1‑141 (MQ=255)                                                                                                                    gTCTTTGTTGATTAAATGATTCTTCGATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTAt                                                                                                <  1:477622/70‑1 (MQ=255)                                                                                                                    gTCTTTGTTGATTAAATGATTCTTCGATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTAt                                                                                                >  2:477622/1‑70 (MQ=255)                                                                                                                    gTCTTTGTTGATTAAATGATTCTTCGATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTAt                                                                                                <  1:477797/70‑1 (MQ=255)                                                                                                                    gTCTTTGTTGATTAAATGATTCTTCGATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTAt                                                                                                >  2:477797/1‑70 (MQ=255)                                                                                                                    gTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTg                         >  2:656456/1‑141 (MQ=255)                                                                                                                     tCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGa                        >  1:758491/1‑141 (MQ=255)                                                                                                                        ttgttgATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATaa                     >  1:145776/1‑141 (MQ=255)                                                                                                                             gATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCATTTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGa                <  1:398611/141‑1 (MQ=255)                                                                                                                                tAAATGATTATTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACaa             >  1:691796/1‑141 (MQ=255)                                                                                                                                 aaaTGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAg            >  1:237076/1‑141 (MQ=255)                                                                                                                                 aaaTGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAg            >  1:237077/1‑141 (MQ=255)                                                                                                                                      aTTGTTCAATTTGTCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAACCTgccctccgcgc       >  2:619679/1‑131 (MQ=255)                                                                                                                                       ttcttcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGttt      >  2:510750/1‑141 (MQ=255)                                                                                                                                       ttcttcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGttt      >  1:291207/1‑141 (MQ=255)                                                                                                                                        tcttcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTa     <  2:673453/141‑1 (MQ=255)                                                                                                                                         cttcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAg    <  1:190339/141‑1 (MQ=255)                                                                                                                                          ttcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAGt   <  2:180313/141‑1 (MQ=255)                                                                                                                                           tcAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAGTa  <  2:420687/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           AACGATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAGTA  >  CP000730/1454743‑1455021

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