Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,190,061	(G)6→7	coding (387/672 nt)	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	1,190,055	1	.	G	98.0%	168.2 / ‑3.4	49	coding (393/672 nt)	phoP	response regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (25/23);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.38e-01

ACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTT  >  NC_000913/1189942‑1190182                                                                                                                   |                                                                                                                                aCCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGaa                                                                                                         >  1:842744/1‑139 (MQ=255)                             tttCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATg                                                                             <  1:471595/139‑1 (MQ=255)                                   taataGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCa                                                                       >  1:49961/1‑139 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGaa                                                                                                                     <  2:1200681/87‑1 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGaa                                                                                                                     >  1:1200681/1‑87 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       >  2:1366544/1‑101 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       <  1:1366544/101‑1 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg                                                                 >  2:996738/1‑139 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg                                                                 >  1:588958/1‑139 (MQ=255)                                         tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg                                                                 >  2:802207/1‑139 (MQ=255)                                           tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       >  1:625503/1‑99 (MQ=255)                                           tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       <  2:625503/99‑1 (MQ=255)                                           tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGcc                                                               >  1:243658/1‑139 (MQ=255)                                           tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGcc                                                               <  1:802207/139‑1 (MQ=255)                                            aTTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       <  1:213952/98‑1 (MQ=255)                                            aTTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc                                                                                                       >  2:213952/1‑98 (MQ=255)                                             ttCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt                                                             <  2:49961/139‑1 (MQ=255)                                               cGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCa                                                           <  2:588958/139‑1 (MQ=255)                                                gAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc                                                          <  2:243658/139‑1 (MQ=255)                                                  aCGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACct                                                        >  1:707553/1‑139 (MQ=255)                                                   cgcgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAcc                                                         >  1:277452/1‑137 (MQ=255)                                                   cgcgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAcc                                                         <  2:277452/137‑1 (MQ=255)                                                     cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc                                                          >  2:1123750/1‑134 (MQ=255)                                                     cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc                                                          <  1:1123750/134‑1 (MQ=255)                                                     cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCtt                                                     <  2:842744/139‑1 (MQ=255)                                                             ttGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGa                                             <  2:1053605/139‑1 (MQ=255)                                                                  cACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACgg                                        >  1:1336553/1‑139 (MQ=255)                                                                    cTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGtt                                      >  2:327188/1‑139 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgcc                                                                                      <  1:411977/89‑1 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgcc                                                                                      >  2:411977/1‑89 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt                                                             <  2:552895/114‑1 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt                                                             >  1:552895/1‑114 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑ggggggga                                                                                                                         >  1:827078/1‑51 (MQ=255)                                                                      tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑ggggggga                                                                                                                         <  2:827078/53‑3 (MQ=255)                                                                          cATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTAt                                                                                            <  2:1063777/79‑1 (MQ=255)                                                                          cATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTAt                                                                                            >  1:1063777/1‑79 (MQ=255)                                                                            ttAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTcaca                              <  2:1336553/139‑1 (MQ=255)                                                                               aTAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGa                                                                                                                 <  2:118595/53‑1 (MQ=255)                                                                               aTAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGa                                                                                                                 >  1:118595/1‑53 (MQ=255)                                                                               aTAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAat                          >  2:140408/1‑139 (MQ=255)                                                                                   aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAatcat                       >  2:527549/1‑139 (MQ=255)                                                                                       ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTc                                 >  1:162472/1‑125 (MQ=255)                                                                                       ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTc                                 <  2:162472/125‑1 (MQ=255)                                                                                       ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATa                            >  2:960827/1‑130 (MQ=255)                                                                                       ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATa                            <  1:960827/130‑1 (MQ=255)                                                                                       ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGc                   >  2:459997/1‑139 (MQ=255)                                                                                                  agagaTCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgccg                                                                                     >  1:1342895/1‑62 (MQ=255)                                                                                                  agagaTCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgccg                                                                                     <  2:1342895/62‑1 (MQ=255)                                                                                                        cAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACtt  <  2:707553/139‑1 (MQ=255)                                                                                                           ccTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGaa                                            <  2:1149743/94‑1 (MQ=255)                                                                                                           ccTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGaa                                            >  1:1149743/1‑94 (MQ=255)                                                                                                                   |                                                                                                                                ACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTT  >  NC_000913/1189942‑1190182

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: ‑