Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,805,475	T→C	N159S (AAT→AGT)	waaP ←	kinase that phosphorylates core heptose of lipopolysaccharide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,805,475	0	T	C	90.1%	205.6 / 11.0	71	N159S (AAT→AGT)	waaP	kinase that phosphorylates core heptose of lipopolysaccharide
Reads supporting (aligned to +/- strand):  ref base T (2/5);  new base C (28/36);  total (30/41)
Fisher's exact test for biased strand distribution p-value = 6.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

CCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATCG  >  NC_000913/3805381‑3805570                                                                                               |                                                                                                ccGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATc                                                                                            <  2:526163/100‑1 (MQ=255)      gCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGc                                                                                       <  1:1381305/100‑1 (MQ=255)       cAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCa                                                                                      >  1:1940215/1‑100 (MQ=255)        aGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAg                                                                                     <  1:481659/100‑1 (MQ=255)          aTCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTa                                                                                   <  2:1492910/100‑1 (MQ=255)           tCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTAt                                                                                  >  2:1525193/1‑100 (MQ=255)           tCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTAt                                                                                  <  1:1439949/100‑1 (MQ=255)            cGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATg                                                                                 <  1:1101697/100‑1 (MQ=255)               tAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCAt                                                                              >  1:70945/1‑100 (MQ=255)                  cTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCAtttt                                                                           >  2:1884952/1‑100 (MQ=255)                  cTGAAATATTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCAtttt                                                                           >  2:1022725/1‑100 (MQ=255)                   tGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTa                                                                          <  2:70945/100‑1 (MQ=255)                    gAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTAc                                                                         >  1:1383171/1‑100 (MQ=255)                    gAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTAc                                                                         <  2:1488773/100‑1 (MQ=255)                    gAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTAc                                                                         <  1:106151/100‑1 (MQ=255)                     aaaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACg                                                                        >  1:569958/1‑100 (MQ=255)                      aaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACg                                                                        <  2:57610/99‑1 (MQ=255)                      aaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGc                                                                       <  2:1646926/100‑1 (MQ=255)                       aTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCa                                                                      >  2:1628635/1‑100 (MQ=255)                         ttttAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCAcc                                                                    >  1:506263/1‑100 (MQ=255)                         ttttAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCAcc                                                                    <  2:1480615/100‑1 (MQ=255)                         ttttAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCAcc                                                                    >  2:261949/1‑100 (MQ=255)                          tttAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCa                                                                   >  1:530546/1‑100 (MQ=255)                             aaTTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAg                                                                >  1:642581/1‑100 (MQ=255)                             aaTTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAg                                                                >  1:1891127/1‑100 (MQ=255)                                tCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTg                                                             <  2:556208/100‑1 (MQ=255)                                 cATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGc                                                            >  2:168910/1‑100 (MQ=255)                                 cATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGc                                                            >  1:451879/1‑100 (MQ=255)                                  aTCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCt                                                           <  2:1885719/100‑1 (MQ=255)                                  aTCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCt                                                           >  2:749323/1‑100 (MQ=255)                                    cTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTac                                                         >  1:1720336/1‑100 (MQ=255)                                    cTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTac                                                         <  1:1530914/100‑1 (MQ=255)                                      tCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTacac                                                       >  1:1598259/1‑100 (MQ=255)                                         cGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTg                                                    <  1:1495262/100‑1 (MQ=255)                                         cGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTg                                                    <  2:1643577/100‑1 (MQ=255)                                          ggCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGc                                                   >  2:436913/1‑100 (MQ=255)                                           gCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCg                                                  <  1:1728470/100‑1 (MQ=255)                                            ccAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGa                                                 <  1:677033/100‑1 (MQ=255)                                             cAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGAt                                                >  1:1505174/1‑100 (MQ=255)                                              aGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATc                                               <  2:548928/100‑1 (MQ=255)                                                tAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAg                                             <  1:1649561/100‑1 (MQ=255)                                                tAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAg                                             <  2:1533743/100‑1 (MQ=255)                                                 aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                            <  2:1616471/100‑1 (MQ=255)                                                  aaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCa                                           <  2:300250/100‑1 (MQ=255)                                                  aaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCa                                           <  1:851718/100‑1 (MQ=255)                                                       cAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGc                                      <  2:848866/100‑1 (MQ=255)                                                        aaaTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCt                                     <  2:375513/100‑1 (MQ=255)                                                        aaaTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCt                                     <  2:723074/100‑1 (MQ=255)                                                        aaaTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCt                                     >  2:203257/1‑100 (MQ=255)                                                          aTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTa                                   >  2:244443/1‑100 (MQ=255)                                                           tGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTaa                                  >  2:1273959/1‑100 (MQ=255)                                                            gAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCCGTATGCATTTTACGCACCATAGTTGCTACACGTGCGTTCAGCATACGCTTa                                   >  2:636409/1‑98 (MQ=255)                                                             aaGCAAAAAGTGGCAAATGTAACAGGCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAaca                                <  1:858804/100‑1 (MQ=255)                                                              aGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAacac                               <  1:1525185/100‑1 (MQ=255)                                                                 aaaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGta                            >  1:1071656/1‑100 (MQ=255)                                                                 aaaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGta                            <  2:214913/100‑1 (MQ=255)                                                                  aaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGta                            <  1:600669/99‑1 (MQ=255)                                                                     aGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATc                        <  1:688945/100‑1 (MQ=255)                                                                        ggCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                     >  2:757449/1‑100 (MQ=255)                                                                        ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                     >  1:1104886/1‑100 (MQ=255)                                                                        ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAg                      >  1:1359628/1‑99 (MQ=255)                                                                          cAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCg                   >  1:1344159/1‑100 (MQ=255)                                                                            aaTGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCggg                 <  1:252425/100‑1 (MQ=255)                                                                            aaTGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCggg                 <  2:569960/100‑1 (MQ=255)                                                                            aaTGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCggg                 <  2:711366/100‑1 (MQ=255)                                                                            aaTGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCggg                 >  2:804612/1‑100 (MQ=255)                                                                             aTGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGt                <  2:193396/100‑1 (MQ=255)                                                                              tGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGtt               <  2:1940228/100‑1 (MQ=255)                                                                                      tCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGccc       <  1:24199/100‑1 (MQ=255)                                                                                         cgGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAAt    <  2:1539952/100‑1 (MQ=255)                                                                                           gTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATCg  <  2:506265/100‑1 (MQ=255)                                                                                               |                                                                                                CCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATCG  >  NC_000913/3805381‑3805570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑