Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,188,861	C→T	V306I (GTA→ATA)	phoQ ←	sensor histidine kinase PhoQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,188,861	0	C	T	100.0%	76.8 / NA	25	V306I (GTA→ATA)	phoQ	sensor histidine kinase PhoQ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/11);  total (14/11)

AGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGTTCTTCCAGTTCGCGGACTTCTTTT  >  NC_000913/1188617‑1189102                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                  aGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGCCAAAGCTGATCTCTGGCGAAATATAGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATCGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCCGCATTATCGGccc                                                                                                                                                                                                                                             >  2:208354/1‑249 (MQ=255)               cACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGc                                                                                                                                                                                                                               >  2:259929/1‑251 (MQ=255)               cACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGc                                                                                                                                                                                                                               >  1:52319/1‑251 (MQ=255)                         aaaTCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTc                                                                                                                                                                                                                     >  2:233168/1‑251 (MQ=255)                                   gCTCACCGACAAAGCTGAGCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAAGTTGCTGTGAAATGCGGCTGATTTGCTCCAGCAGTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCaga                                                                                                                                                                                                           <  1:178138/251‑1 (MQ=255)                                       aCCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAAc                                                                                                                                                                                                       <  1:300900/251‑1 (MQ=255)                                                      ctctGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGATCATCTTTTCACTACGCAGAGAACGCAGCGGACTTTgcc                                                                                                                                                                                        >  2:80717/1‑250 (MQ=255)                                                        ctGGCGAAAGATCGAGAGAGATAGTGCCCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACttt                                                                                                                                                                                           <  2:224562/246‑1 (MQ=255)                                                                   tCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTgg                                                                                                                                                                           >  2:96485/1‑251 (MQ=255)                                                                                     ccTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGt                                                                                                                                                         >  1:283530/1‑251 (MQ=255)                                                                                               gATACCCTTTGTTCAGCGCTGAGTTGAGTTTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCATGGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGGGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACGGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTg                                                                                                                                               <  1:259929/251‑1 (MQ=255)                                                                                                   cacTTTGTTCAGAGCTGAGGAGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGCGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGcg                                                                                                                                           >  1:92399/1‑251 (MQ=255)                                                                                                                         agaTTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACg                                                                                                                     >  2:209840/1‑251 (MQ=255)                                                                                                                                       tGGGGCTACCGGTTGCACCTCTTGGTTGAGCAATTTCCCGCCGGGCTTCCAGGCACGAGCCTGGTAGTAGCCAACTTGAGGTAACATGCGACTGATTTGCTCCATGATTATGGGCTCAGCTCCATGGACGCTCATCTTTTCACTCCGCATATAACGCAGCTTACTTTTCGGCTCCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCTTCGTACGGTATTTGTCGTAACGTTCGCGTTCACtt                                                                                                        <  1:262708/250‑1 (MQ=255)                                                                                                                                                       agctaggggcggAGCAATGCCCCGCCGCGCATCCTGGCCCGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCTTTATCGGCTCAGCATCACGGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAg                                                                                       <  1:214454/240‑1 (MQ=255)                                                                                                                                                             gggCTGAGCAATGCCCCGCCGCGCATCCTGGCACGATGCAGGTAGTAGCCAATTTGCTGTAAAATGCGGCTGATTTGCTCCACCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTGGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCg                                                                                 <  1:217232/250‑1 (MQ=255)                                                                                                                                                              ggcggAGCAAGGCCCCGCCGCGCATCCTGGCTGGATGAAGGTAGTAGCCAATTTGCGGGGAAATGCGGCTGATTTGCCCCAGCATTATCGGCTCAGCATCCCTGACGCTCATCTTTTCCCTACGCAGAGAACGCGGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt                                                                                <  2:52319/247‑1 (MQ=255)                                                                                                                                                                                   gcATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgc                                                           >  1:268047/1‑251 (MQ=255)                                                                                                                                                                                               gATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTggg                                               >  2:59499/1‑250 (MQ=255)                                                                                                                                                                                                       tagtagCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCa                                        >  1:219187/1‑250 (MQ=255)                                                                                                                                                                                                                aTTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGtt                              >  2:237977/1‑251 (MQ=255)                                                                                                                                                                                                                        ggAAATGCGGCTGATTTGCACCAGCATGATCGGCACAGCATCACTGACGCTCATCTTTTCATTCCGCAGAGAACGCAGCGTACTTTGCAGCCCCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGttctt                      <  1:80717/250‑1 (MQ=255)                                                                                                                                                                                                                                 gCTGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGTTCTTCCAGTTcgc             >  1:45710/1‑251 (MQ=255)                                                                                                                                                                                                                                   tGATTTGCTCCAGCATTATCGGCTCAGCATCACTGACGCTCATTTTTTCACTGCGCAGAGAACGCAGCTTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGTTCTTCCAGTTcgcg            <  2:106689/250‑1 (MQ=255)                                                                                                                                                                                                                                            ccAGCATTATCGGCTCAGCATCCCTGACGCTCATCTTTTCCCTACGCAGAGAACGCAGCGTCCTTTGAAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGTTCTTCCAGTTCGCGGACTTCtttt  <  2:219187/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                  AGCACGTTGCCCATCACCTCGACAAAATCGTTCTGCTCACCGACAAAGCTGATCTCTGGCGAAATATCGAGAGAGATATTGACCCCTTTGCGTTGATACACTTTGTTCAGCGCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGAGCAATTCGCGGTTATGTTCTTCCAGTTCGCGGACTTCTTTT  >  NC_000913/1188617‑1189102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑