Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,190,144	G→A	P102S (CCG→TCG)	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	1,190,144	0	G	A	100.0%	180.7 / NA	57	P102S (CCG→TCG)	phoP	response regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/27);  total (30/27)

TTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190010‑1190278                                                                                                                                       |                                                                                                                                       ttCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTa                                                                                                                                    >  1:174091/1‑139 (MQ=255)  tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   >  2:952018/1‑139 (MQ=255)   cGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 <  2:346326/139‑1 (MQ=255)               aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTcaca                                                                                                                              <  2:125483/131‑1 (MQ=255)               aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTcaca                                                                                                                              >  1:125483/1‑131 (MQ=255)                   ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:269710/1‑139 (MQ=255)                   ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:541948/1‑139 (MQ=255)                   ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:953922/1‑139 (MQ=255)                    tCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  1:952018/139‑1 (MQ=255)                    tCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAGCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  2:953922/139‑1 (MQ=255)                              agagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTaa                                                                                                       >  1:741765/1‑139 (MQ=255)                                   tCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACtt                                                                                                  <  2:741765/139‑1 (MQ=255)                                                  gggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGc                                                                                    >  2:372760/1‑138 (MQ=255)                                                  gggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGc                                                                                    <  1:372760/138‑1 (MQ=255)                                                              aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:672053/139‑1 (MQ=255)                                                              aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1142968/139‑1 (MQ=255)                                                               ccTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:123250/1‑138 (MQ=255)                                                               ccTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:123250/138‑1 (MQ=255)                                                                 tgtgAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:1042085/1‑136 (MQ=255)                                                                 tgtgAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1042085/136‑1 (MQ=255)                                                                           gACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAg                                                          >  1:59692/1‑139 (MQ=255)                                                                                   ttACGCCCCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCa                                                  <  2:269710/139‑1 (MQ=255)                                                                                      cgccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:802198/115‑1 (MQ=255)                                                                                      cgccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGAATTTGTCCTGCCAGCTTTCACggg                                                                       >  1:802198/1‑115 (MQ=255)                                                                                        ccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAat                                                                                                                          <  1:490624/62‑1 (MQ=255)                                                                                        ccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAat                                                                                                                          >  2:490624/1‑62 (MQ=255)                                                                                           cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAAt                                                       <  2:981111/126‑1 (MQ=255)                                                                                           cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAAt                                                       >  1:981111/1‑126 (MQ=255)                                                                                           cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACa                                          >  2:524197/1‑139 (MQ=255)                                                                                               aaTGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGt                                      <  1:524197/139‑1 (MQ=255)                                                                                                aTGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGtt                                     >  1:328877/1‑139 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAACCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCgg                                                    <  1:354251/119‑1 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAACCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCgg                                                    >  2:354251/1‑119 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 <  1:345987/42‑1 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 >  2:345987/1‑42 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  2:1253117/58‑1 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 >  1:1253117/1‑58 (MQ=255)                                                                                                     tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTAc                                >  2:863344/1‑139 (MQ=255)                                                                                                      gCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1107767/99‑1 (MQ=255)                                                                                                      gCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:1107767/1‑99 (MQ=255)                                                                                                       cATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGc                              >  2:176121/1‑139 (MQ=255)                                                                                                             cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACtt                                                                                                         <  2:289299/58‑1 (MQ=255)                                                                                                             cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACtt                                                                                                         >  1:289299/1‑58 (MQ=255)                                                                                                              gcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAgcggc                       <  2:541948/139‑1 (MQ=255)                                                                                                                 aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               <  2:1116753/48‑1 (MQ=255)                                                                                                                 aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               >  1:1116753/1‑48 (MQ=255)                                                                                                                 aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGaa                    >  1:1001217/1‑139 (MQ=255)                                                                                                                  tCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAAt                   <  2:174091/139‑1 (MQ=255)                                                                                                                               atGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCg      <  2:328877/139‑1 (MQ=255)                                                                                                                                tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGt     <  1:176121/139‑1 (MQ=255)                                                                                                                                tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGt     >  1:953430/1‑139 (MQ=255)                                                                                                                                 gAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTc    >  1:1185869/1‑139 (MQ=255)                                                                                                                                   aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       >  2:468773/1‑54 (MQ=255)                                                                                                                                   aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       <  1:468773/54‑1 (MQ=255)                                                                                                                                   aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTGCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCt  >  2:134987/1‑139 (MQ=255)                                                                                                                                   aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGt                                                                   <  1:364340/74‑1 (MQ=255)                                                                                                                                   aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGt                                                                   >  2:364340/1‑74 (MQ=255)                                                                                                                                       |                                                                                                                                       TTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190010‑1190278

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: ‑