Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,483,411	G→T	L117L (CTG→CTT)	hrpA →	ATP‑dependent RNA helicase HrpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,483,411	0	G	T	100.0%	125.6 / NA	37	L117L (CTG→CTT)	hrpA	ATP‑dependent RNA helicase HrpA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (18/19);  total (18/19)

TATCCTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTGGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTGCGTTTC  >  NC_000913/1483277‑1483540                                                                                                                                       |                                                                                                                                  tATCCTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGgcg                                                                                                                              <  2:452831/140‑1 (MQ=255)   tCCTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGcgcg                                                                                                                            >  1:102460/1‑140 (MQ=255)    ccTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAGACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCgg                                                                                                                           <  1:489757/140‑1 (MQ=255)    ccTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCgg                                                                                                                           >  1:240793/1‑140 (MQ=255)       gACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGAt                                                                                                                        <  2:98750/140‑1 (MQ=255)       gACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGAt                                                                                                                        >  2:82214/1‑140 (MQ=255)        aCAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGAtt                                                                                                                       >  2:593589/1‑140 (MQ=255)         cAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTa                                                                                                                      <  2:648281/140‑1 (MQ=255)            tttACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAg                                                                                                                   <  2:671938/140‑1 (MQ=255)                    ttAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTAGCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGAtg                                                                                                           >  2:616379/1‑139 (MQ=255)                       gTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGc                                                                                                        >  1:636642/1‑140 (MQ=255)                                      aCATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGcgt                                                                                         >  2:296658/1‑140 (MQ=255)                                      aCATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGcgt                                                                                         >  2:29114/1‑140 (MQ=255)                                          tctcGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCgtcgtc                                                                                     >  2:524237/1‑140 (MQ=255)                                            tcGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTg                                                                                   <  1:593589/140‑1 (MQ=255)                                            tcGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTg                                                                                   >  2:475337/1‑140 (MQ=255)                                              gAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTggc                                                                                 <  2:684599/140‑1 (MQ=255)                                                    aTTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAg                                                                           >  1:402109/1‑140 (MQ=255)                                                      tCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGaa                                                                         <  1:524237/140‑1 (MQ=255)                                                           aTCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTg                                                                    <  2:373749/140‑1 (MQ=255)                                                           aTCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTg                                                                    <  2:402109/140‑1 (MQ=255)                                                              aCCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCg                                                                 >  2:512988/1‑140 (MQ=255)                                                                cAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGaa                                                               <  2:669691/140‑1 (MQ=255)                                                                      gtgATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTAt                                                         <  1:296658/140‑1 (MQ=255)                                                                       tgATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTAtt                                                        >  1:182205/1‑140 (MQ=255)                                                                        gATCGTTTCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTg                                                       >  2:436086/1‑140 (MQ=255)                                                                           cgtcgCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCgg                                                    <  1:69758/140‑1 (MQ=255)                                                                              cgCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAag                                                 >  1:112565/1‑140 (MQ=255)                                                                                  ggggAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCt                                             <  1:475337/140‑1 (MQ=255)                                                                                    ggAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGa                                           >  2:284740/1‑140 (MQ=255)                                                                                     gAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGaa                                          >  2:583798/1‑140 (MQ=255)                                                                                               cTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCg                                <  2:203119/140‑1 (MQ=255)                                                                                                 ggTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCggg                              <  2:102460/140‑1 (MQ=255)                                                                                                        cGACTCAGTTACCGAAAATCCGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGc                       <  2:40614/140‑1 (MQ=255)                                                                                                            tCAGTTACCGAAAATCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCg                   >  1:741106/1‑140 (MQ=255)                                                                                                                      aaaaTCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGt         <  1:436086/140‑1 (MQ=255)                                                                                                                       aaaTCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTg        <  1:583798/140‑1 (MQ=255)                                                                                                                          tCTGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTGCGt     >  2:517246/1‑140 (MQ=255)                                                                                                                            tGTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTGCGttt   <  1:29114/140‑1 (MQ=255)                                                                                                                             gTATGGAGCTTGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTGCGTTTc  >  2:584199/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                  TATCCTGACAATTTACCGGTTAGTCAGAAAAAACAGGACATTCTCGAAGCGATTCGTGATCACCAGGTGGTGATCGTCGCCGGGGAAACGGGTTCTGGTAAAACGACTCAGTTACCGAAAATCTGTATGGAGCTGGGGCGCGGGATTAAAGGACTGATCGGCCATACCCAGCCGCGTCGTCTGGCGGCAAGAACAGTGGCGAACCGTATTGCGGAAGAGCTGAAAACGGAGCCGGGCGGTTGCATCGGTTACAAAGTGCGTTTC  >  NC_000913/1483277‑1483540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑