Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,095,230	G→T	S251R (AGC→AGA)	rhaA ←	L‑rhamnose isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,095,230	0	G	T	100.0%	140.6 / NA	40	S251R (AGC→AGA)	rhaA	L‑rhamnose isomerase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (15/25);  total (15/25)

GATCGCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGGCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCATCCAGTGCT  >  NC_000913/4095094‑4095365                                                                                                                                         |                                                                                                                                        gATCGCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCtg                                                                                                                                      <  2:417080/140‑1 (MQ=255)   tCGCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCtggg                                                                                                                                    >  2:360134/1‑139 (MQ=255)    cGCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCtggtg                                                                                                                                   >  2:429091/1‑140 (MQ=255)     gCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCtggtgg                                                                                                                                  >  2:435476/1‑140 (MQ=255)     gCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCtggtgg                                                                                                                                  >  2:372739/1‑140 (MQ=255)      cTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGc                                                                                                                                 >  2:583037/1‑140 (MQ=255)      cTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGc                                                                                                                                 <  1:372739/140‑1 (MQ=255)      cTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGc                                                                                                                                 <  1:435476/140‑1 (MQ=255)             aGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATAcccc                                                                                                                          <  2:628419/140‑1 (MQ=255)                   ccGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGc                                                                                                                                 <  1:125957/127‑1 (MQ=255)                   ccGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGc                                                                                                                                 >  2:125957/1‑127 (MQ=255)                       aCGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACt                                                                                                                >  1:246796/1‑140 (MQ=255)                         ggCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCa                                                                                                              <  1:376579/140‑1 (MQ=255)                              aCGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGa                                                                                                         <  1:389516/140‑1 (MQ=255)                                gTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGc                                                                                                       <  2:287738/140‑1 (MQ=255)                                   cagcagcaACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCaa                                                                                                    <  1:448167/140‑1 (MQ=255)                                           aCTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAg                                                                                            <  1:429091/140‑1 (MQ=255)                                                     aTACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTgcgc                                                                                  <  1:379438/140‑1 (MQ=255)                                                       aCAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCa                                                                                <  1:39050/140‑1 (MQ=255)                                                              ggcggcGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGctctct                                                                                      <  1:252657/127‑1 (MQ=255)                                                              ggcggcGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGctctct                                                                                      >  2:252657/1‑127 (MQ=255)                                                              ggcggcGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCaa                                                                         >  1:94492/1‑140 (MQ=255)                                                              ggcggcGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCaa                                                                         >  1:329544/1‑140 (MQ=255)                                                                cggcggAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAAc                                                                       >  2:563794/1‑140 (MQ=255)                                                                cggcggAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAAc                                                                       >  1:424081/1‑140 (MQ=255)                                                                cggcggAAATCTTGTCGGAAATCAATTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCACGTAAAACTCATTGGAGCCCACCGAGCTCTTCTCTGCGCCAAAGCCAGAc                                                                       >  2:646956/1‑140 (MQ=255)                                                                   cggAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGcc                                                                           >  1:4112/1‑133 (MQ=255)                                                                   cggAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGcc                                                                           <  2:4112/133‑1 (MQ=255)                                                                              tCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAAc                                                         <  2:94492/140‑1 (MQ=255)                                                                              tCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAAc                                                         <  1:259840/140‑1 (MQ=255)                                                                              tCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAAc                                                         <  2:329544/140‑1 (MQ=255)                                                                                ggAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACgg                                                       <  1:163354/140‑1 (MQ=255)                                                                                               cGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTgcg                                        <  1:563794/140‑1 (MQ=255)                                                                                               cGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTgcg                                        <  2:246796/140‑1 (MQ=255)                                                                                                            ccGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCtt                           <  2:394797/140‑1 (MQ=255)                                                                                                            ccGGCGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCtt                           <  2:349797/140‑1 (MQ=255)                                                                                                                cGTCCAGGCACAGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCg                       <  1:369137/140‑1 (MQ=255)                                                                                                                        cacaGCGCAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCAc               <  1:583037/140‑1 (MQ=255)                                                                                                                             cgcAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCAt          >  2:170615/1‑140 (MQ=255)                                                                                                                             cgcAGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCAt          >  2:213931/1‑140 (MQ=255)                                                                                                                                aGTCTGGCGTCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCATCCa       <  2:465856/140‑1 (MQ=255)                                                                                                                                     ggcgtcTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCATCCAGtgct  >  1:113727/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                        GATCGCTGTCCCAGCGAACCGGACGGCTGACGTGCAGCAGCAACTGCGGCACATACAGCATGGCGGCGGAAATCTTGTCGGAAATCACTTCAGTCGGGTGGAAGTGCCCGGCGTCCAGGCACAGCGCAGTCTGGCGGCTGGTGGCATACCCCATGTAAAACTCATTGGAGCCAACCGTGTAGCTCTCTGCGCCAATGCCAAACAATTTGCTCTCAACGGCGTCGATATGGTGCGCAGGGTTTAGCTTCTCGCTGATCACCTCATCCAGTGCT  >  NC_000913/4095094‑4095365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑