Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,190,263	A→G	L62P (CTG→CCG)	phoP ←	response regulator in two‑component regulatory system with PhoQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,190,263	0	A	G	100.0%	144.0 / NA	38	L62P (CTG→CCG)	phoP	response regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (19/19);  total (19/19)

TCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTGCGTCATCGACCTGATGACCAGCATCCTGAATCT  >  NC_000913/1190131‑1190392                                                                                                                                     |                                                                                                                                  tCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACa                                                                                                                             <  2:152226/139‑1 (MQ=255)   aaTATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGa                                                                                                                           <  2:560599/139‑1 (MQ=255)     tatGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGAcc                                                                                                                         >  1:532199/1‑139 (MQ=255)          aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTGATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCACTGAAATATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCg                                                                                                                        <  1:539434/135‑1 (MQ=255)          aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCg                                                                                                                        >  2:539434/1‑135 (MQ=255)          aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCt                                                                                                                    >  2:166210/1‑139 (MQ=255)          aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCt                                                                                                                    >  1:255699/1‑139 (MQ=255)          aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCt                                                                                                                    >  1:288764/1‑139 (MQ=255)               tttAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCt                                                                                                               >  1:293822/1‑139 (MQ=255)                                      cGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTgg                                                                                                             <  2:161949/118‑1 (MQ=255)                                      cGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTgg                                                                                                             >  1:161949/1‑118 (MQ=255)                                      cGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGc                                                                                        >  1:533752/1‑139 (MQ=255)                                      cGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGc                                                                                        >  1:596163/1‑139 (MQ=255)                                       ggCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCa                                                                                       <  1:163724/139‑1 (MQ=255)                                       ggCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCa                                                                                       >  2:671938/1‑139 (MQ=255)                                       ggCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCa                                                                                       <  1:645781/139‑1 (MQ=255)                                          aCTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAata                                                                                    <  2:288764/139‑1 (MQ=255)                                          aCTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAata                                                                                    <  2:293822/139‑1 (MQ=255)                                            ttAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATc                                                                                  <  2:255699/139‑1 (MQ=255)                                                 aCTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGta                                                                             <  1:549716/139‑1 (MQ=255)                                                 aCTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGta                                                                             <  1:671938/139‑1 (MQ=255)                                                   ttCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATAACCGGtata                                                                           >  1:196420/1‑139 (MQ=255)                                                     cGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATg                                                                         <  2:701925/139‑1 (MQ=255)                                                      gACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGt                                                                        >  1:241327/1‑139 (MQ=255)                                                      gACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGt                                                                        >  1:236284/1‑139 (MQ=255)                                                          ttGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCAt                                                                    <  2:596163/139‑1 (MQ=255)                                                           tGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCAtt                                                                   <  2:241327/139‑1 (MQ=255)                                                           tGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCAtt                                                                   <  2:532199/139‑1 (MQ=255)                                                                      cTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATaataat                                                        >  1:207793/1‑139 (MQ=255)                                                                              ggCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGcttct                                                <  1:166210/139‑1 (MQ=255)                                                                                         ccAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCaa                                                                                      >  2:80396/1‑90 (MQ=255)                                                                                         ccAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCaa                                                                                      <  1:80396/90‑1 (MQ=255)                                                                                           aGAATCGGCAGTTAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTg                                   <  2:797352/139‑1 (MQ=255)                                                                                             aaTCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTGCg                                 >  1:23807/1‑139 (MQ=255)                                                                                                                  gCTACGCCAGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTGCGTCATCGACCTGATTACCAGCa            >  2:443691/1‑139 (MQ=255)                                                                                                                          aGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCAtt                                                                   <  2:40700/76‑1 (MQ=255)                                                                                                                          aGCGGCGAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCAtt                                                                   >  1:40700/1‑76 (MQ=255)                                                                                                                            cggcgAATCGGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTGCGTCATCGACCTGATGACCAGCATCCTGAATCt  >  2:77738/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                  TCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCTCGTCTGGCAATCCGAGATCGACAATCGCAATATCCGGTATATGTTCATTGAGATAATAATCGGCTTCTTTGGCATCTTCTGCGTCATCGACCTGATGACCAGCATCCTGAATCT  >  NC_000913/1190131‑1190392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑