Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,026,655	C→T	100%	E87K (GAA→AAA)	vraR ←	response regulator VraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,026,655	0	C	T	100.0%	194.0 / NA	62	E87K (GAA→AAA)	vraR	response regulator VraR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/32);  total (30/32)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGG  >  CP000730/2026519‑2026789                                                                                                                                         |                                                                                                                                       aCTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAAt                                                                                                                                     >  2:481925/1‑140 (MQ=255)   taagtcttccgtgccAAAAACAGATCCTCCTCTAGTAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGCTGCTTTTACAATGTAACTATCGACACCTGCACCTAATGCACCATATACCTCTTTATCTTtaataa                                                                                                                                   <  2:113096/126‑1 (MQ=255)    aaaaCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATaaa                                                                                                                                  >  2:54854/1‑140 (MQ=255)      aaCTTCCGGTTCAAAAGCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAAc                                                                                                                                <  1:432015/140‑1 (MQ=255)       aCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACt                                                                                                                               <  2:190627/140‑1 (MQ=255)       aCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATATAATGCACGATATACCTCTTTATCTTTAATAAAACt                                                                                                                               <  2:173867/140‑1 (MQ=255)        cTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTa                                                                                                                              <  2:66738/140‑1 (MQ=255)        cTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTa                                                                                                                              <  1:237780/140‑1 (MQ=255)        cTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAAGATAACGATCGACACCTGCATCTACTGCACGATATACCTCTTTATCTTTAATAAAACTa                                                                                                                              <  1:381019/140‑1 (MQ=255)           ccGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATAGCTTTTGAACTTGTTGTTTTTAAAATGTAACTATCGACAACTGCATCTAATGCACGATCTACCTCTTTATCTTTAATAAAACTAGtt                                                                                                                           >  2:322979/1‑140 (MQ=255)           ccGGTTCAAAAACAGATTCTCCTCTAGAAGTGTTACGAACTGCATAGGCGAGAGCTTTTGCACTTGTTGTTTTTAAAATGTAGCGATCGACACCTGCATCCAATGCACGATATACCTCTTTATGTTTAATAAAACTAGtt                                                                                                                           >  2:322973/1‑140 (MQ=255)            cGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGCCACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTa                                                                                                                          >  1:697974/1‑140 (MQ=255)                      aCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATAc                                                                                                                <  2:644395/140‑1 (MQ=255)                      aCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATAc                                                                                                                >  1:438488/1‑140 (MQ=255)                        aGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACtt                                                                                                              >  1:637610/1‑140 (MQ=255)                             ctcctcTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAAtt                                                                                                         <  1:685306/140‑1 (MQ=255)                             ctcctcTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAAtt                                                                                                         >  1:551513/1‑140 (MQ=255)                             ctcctcTAGAAGTTTTACGAACTGCATCGGCGAAATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAAtt                                                                                                         >  2:400480/1‑140 (MQ=255)                                  ctAGTAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCgg                                                                                                    <  1:174873/140‑1 (MQ=255)                                   gaGAAGTTTTACGACCTGGATAGGCTCTATCTTTTGCACTTTTTGTTTTTAAAATGTAACTATCGACACCCGCATCTAAAGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAAAACTTTAATCTGCAGt                                                                                                   <  2:273273/139‑1 (MQ=255)                                       aGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACATGCATCTAATGCACGATATACATCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATCTACGGTAAAt                                                                                               >  2:311499/1‑140 (MQ=255)                                          tttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCGCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtt                                                                                            >  1:17345/1‑140 (MQ=255)                                              cGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttttt                                                                                        >  2:240322/1‑140 (MQ=255)                                              cGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttttt                                                                                        >  1:407704/1‑140 (MQ=255)                                                aagctcttCGGCTATATCTTTTGCGCTTTTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAACAAAACTTATTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTaa                                                                                      <  2:454601/133‑1 (MQ=255)                                                  cTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACATGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATc                                                                                    >  1:484851/1‑140 (MQ=255)                                                   tGCATCGGCGATATCTTTTGCACTTTTTGTTTTTAAAATCTAAGTAGCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCt                                                                                   <  1:313067/140‑1 (MQ=255)                                                      aTCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAg                                                                                <  1:287008/140‑1 (MQ=255)                                                      aTCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAg                                                                                <  1:398674/140‑1 (MQ=255)                                                       tCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATACAAATAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTAAgt                                                                               >  1:660576/1‑140 (MQ=255)                                                       tCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACAAAATACCGCTTTATCTTTTATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgt                                                                               <  1:530951/140‑1 (MQ=255)                                                        cGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgtc                                                                              <  1:589057/140‑1 (MQ=255)                                                         ggCGATTTCTTTTGCACCTGTTGGTTTTAAAATGTAACTATCGACAACTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgtcg                                                                             <  2:675906/140‑1 (MQ=255)                                                            gATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACAGTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGtcgtcg                                                                          <  1:398022/140‑1 (MQ=255)                                                              tatCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCt                                                                        >  1:669275/1‑140 (MQ=255)                                                                 tctttGCTCTTGGTGTTTTTAAAATGTAACTATCGACACCTGCATCTAAGTCACGTTATACCTCTTTATCTTTAAGAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTGTAATCTGAGTCGTCGCTTCt                                                                     <  2:136382/138‑1 (MQ=255)                                                                 ctcttGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCt                                                                     <  2:487358/137‑1 (MQ=255)                                                                  ttttGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGCGTCGTCGTTTCtc                                                                    >  1:449334/1‑139 (MQ=255)                                                                    ttGCACTTGTTTGTTTTACAATGTAACTATCGACACCTGCATGTAATGCACGATATACCTCTGTATCTTTAATCAAACTAGTTAACATTAATTCTTTAATTTGCGGTAGATCTTTCTTAATCTGGGTCGTCGCTTGTaca                                                                  <  2:287373/140‑1 (MQ=255)                                                                    ttGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCGTTTTTAAGCTGAGTCGTCGCTTCTaca                                                                  <  1:15458/140‑1 (MQ=255)                                                                    ttGCACGTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTaca                                                                  <  2:697974/140‑1 (MQ=255)                                                                           tgttgtTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACAccatcca                                                           <  2:438488/140‑1 (MQ=255)                                                                           tgttgtTTCTAAAATGTAACTATAGACACCTCCATCTTATGCACGTAATTCCTCTTTGTCTTTAATAAAACTAGTTAACCTTAGTCCTTTAATTTTCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACAccatcca                                                           <  2:102688/140‑1 (MQ=255)                                                                               gttTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCATCGCTTCTACACCATCCATGTc                                                       >  1:443695/1‑140 (MQ=255)                                                                                tttttAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATACATGttt                                                      >  2:725982/1‑138 (MQ=255)                                                                                          gTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTa                                            <  2:673476/140‑1 (MQ=255)                                                                                               tATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATcc                                       >  2:255360/1‑140 (MQ=255)                                                                                                     cacCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCattaac                                 >  1:562581/1‑139 (MQ=255)                                                                                                     cacCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCattaaa                                 <  2:353054/140‑1 (MQ=255)                                                                                                      acCTGCATCTAATGCACGATATACCTTTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCataaaaa                                >  2:451372/1‑140 (MQ=255)                                                                                                          gCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCattaaaattaa                            <  1:54854/140‑1 (MQ=255)                                                                                                          gCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACAAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTACTATGAGATGTAGCCTCTACACCATCCATGTCATCAATCAGTAACTCCattaaaattaa                            >  1:494533/1‑140 (MQ=255)                                                                                                              gtAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCt                        <  2:401446/139‑1 (MQ=255)                                                                                                              cTACTGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCt                        <  2:175864/140‑1 (MQ=255)                                                                                                              cTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAActct                        >  2:421521/1‑140 (MQ=255)                                                                                                                 aTGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACCTTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTACATCTGGc                     >  1:21091/1‑140 (MQ=255)                                                                                                                 aTGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGACTCGTCGCTTCTACACCCTCCATGTCATCCATAACTAAACCCAATAAAATAAAATcccgc                     >  2:80583/1‑136 (MQ=255)                                                                                                                  tGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTTCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCTTCCATAAGTAACTCCATTAAAATTAAATCTGGCt                    >  1:341916/1‑140 (MQ=255)                                                                                                                   gCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTCAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCtt                   >  2:526866/1‑140 (MQ=255)                                                                                                                          ataCCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGCTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa            >  1:44401/1‑140 (MQ=255)                                                                                                                              ctttttATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTTAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATggg        <  2:496328/137‑1 (MQ=255)                                                                                                                              ctctTTATCTTTATTAAAACTAGTTAACATTAATACTTTAATTTGGGGTCACTATTATTAAATGTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATggg        <  2:696454/140‑1 (MQ=255)                                                                                                                                    aTCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTgg  >  2:641117/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                       ACTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGG  >  CP000730/2026519‑2026789

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑