Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,319,449	T→C	N143S (AAC→AGC)	rcsC ←	sensory histidine kinase RcsC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,319,449	0	T	C	100.0%	95.4 / NA	28	N143S (AAC→AGC)	rcsC	sensory histidine kinase RcsC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/16);  total (12/16)

TATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACG  >  NC_000913/2319312‑2319575                                                                                                                                          |                                                                                                                               tATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGctt                                                                                                                              <  1:709651/140‑1 (MQ=255)                cATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCa                                                                                                               >  2:455608/1‑140 (MQ=255)                          tttattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTAt                                                                                                     <  1:289902/140‑1 (MQ=255)                                 aTGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCa                                                                                              <  2:47352/140‑1 (MQ=255)                                  tGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGACATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAg                                                                                             >  1:657743/1‑140 (MQ=255)                                   gCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGt                                                                                            <  1:320654/140‑1 (MQ=255)                                      ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                         >  1:516117/1‑140 (MQ=255)                                      ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                         >  1:612928/1‑140 (MQ=255)                                      ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                         >  2:502136/1‑140 (MQ=255)                                        cATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgcgc                                                                                       >  1:642360/1‑140 (MQ=255)                                             aaaGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATaaa                                                                                  <  2:642360/140‑1 (MQ=255)                                             aaaGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATaaa                                                                                  <  2:612928/140‑1 (MQ=255)                                               aGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAAcc                                                                                <  1:374920/140‑1 (MQ=255)                                               aGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAAcc                                                                                <  1:455608/140‑1 (MQ=255)                                               aGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAAcc                                                                                <  1:502136/140‑1 (MQ=255)                                                       aCGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                        <  2:549742/140‑1 (MQ=255)                                                                    ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCGGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                           <  2:474207/140‑1 (MQ=255)                                                                    ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                           <  2:340670/140‑1 (MQ=255)                                                                       cACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                        >  2:62546/1‑124 (MQ=255)                                                                       cACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                        <  1:62546/124‑1 (MQ=255)                                                                          tGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGcc                                                     <  1:393745/140‑1 (MQ=255)                                                                                         aCCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTg                                      >  2:452949/1‑140 (MQ=255)                                                                                           cGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCg                                    >  1:16283/1‑140 (MQ=255)                                                                                                  ggCCATGCAGAGGATAGCGCTGCCGATTAAAAATACCCGACTTATTTCGTAAGCCGCAGAAAAATTAGCGCGCCAGTACCGCAAGAACCACGCCAATGACCCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAAt                             <  2:318464/140‑1 (MQ=255)                                                                                                   gCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATc                            <  2:16283/140‑1 (MQ=255)                                                                                                     cATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCgg                          >  2:358388/1‑140 (MQ=255)                                                                                                          agagGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCg                     <  2:657743/140‑1 (MQ=255)                                                                                                                 aTCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACa              >  2:517608/1‑140 (MQ=255)                                                                                                                           aTTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCaaa    >  2:190390/1‑140 (MQ=255)                                                                                                                             tAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACg  <  2:77286/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                               TATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACG  >  NC_000913/2319312‑2319575

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: ‑