Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,903,571	A→G	T164A (ACC→GCC)	manY →	mannose‑specific enzyme IIC component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,903,571	0	A	G	97.1%	225.4 / ‑2.5	68	T164A (ACC→GCC)	manY	mannose‑specific enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (30/36);  total (30/38)
Fisher's exact test for biased strand distribution p-value = 5.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-01

CAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGA  >  NC_000913/1903474‑1903667                                                                                                  |                                                                                                 cAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATACGTGTGACTATTCCGGCCGTAATCGTTGCGCTGTCTGTTGGTGcc                                                                                                >  2:1373248/1‑100 (MQ=255)     ntGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCATGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCg                                                                                            >  1:888266/2‑100 (MQ=255)     cTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCg                                                                                            >  2:731365/1‑100 (MQ=255)     cTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCg                                                                                            >  1:1090690/1‑100 (MQ=255)      tGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGa                                                                                           >  2:1552655/1‑100 (MQ=255)      tGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGa                                                                                           >  1:1809749/1‑100 (MQ=255)      tGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGa                                                                                           <  1:1597342/100‑1 (MQ=255)         cAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGt                                                                                        <  1:400075/100‑1 (MQ=255)           gCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTAc                                                                                      >  2:104222/1‑100 (MQ=255)           gCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTAc                                                                                      >  2:1027243/1‑100 (MQ=255)             gATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAg                                                                                    >  2:1052422/1‑100 (MQ=255)             gATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAg                                                                                    <  2:1044390/100‑1 (MQ=255)                     ggATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCt                                                                            >  1:1706058/1‑100 (MQ=255)                     ggATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCt                                                                            <  2:1493106/100‑1 (MQ=255)                      gATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTg                                                                           <  2:1455970/100‑1 (MQ=255)                         ccACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAAt                                                                        >  1:1781890/1‑100 (MQ=255)                          cACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTTGCTATTCCGGCCGTTATCGTTGCTCTGTCTTTTTGTGCCAGCTAAGTACAGAACATGCTGAATg                                                                       <  1:1035250/100‑1 (MQ=255)                          cACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATg                                                                       <  1:667771/100‑1 (MQ=255)                            cGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCg                                                                     <  1:271225/100‑1 (MQ=255)                                 cttctCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTcc                                                                >  2:191362/1‑100 (MQ=255)                                 cttctCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTcc                                                                >  2:670931/1‑100 (MQ=255)                                    ctctGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGa                                                             >  2:41380/1‑100 (MQ=255)                                     tctGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGaa                                                            <  2:1050616/100‑1 (MQ=255)                                     tctGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGaa                                                            <  2:1147357/100‑1 (MQ=255)                                      ctGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAg                                                           >  1:1228441/1‑100 (MQ=255)                                         ttCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtgg                                                        <  2:176628/100‑1 (MQ=255)                                          tCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggt                                                       >  1:114029/1‑100 (MQ=255)                                           ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                      >  1:933213/1‑100 (MQ=255)                                           ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGCCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                      >  2:1724154/1‑100 (MQ=255)                                            cTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGGACATGCTGAATGCGATTCCGGAAGTGGTGa                                                     <  2:1738486/100‑1 (MQ=255)                                             tGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAc                                                    >  1:1805199/1‑100 (MQ=255)                                              gcaagcaaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAcc                                                   >  1:388265/1‑100 (MQ=255)                                                aagcaaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCaa                                                 >  1:1312735/1‑100 (MQ=255)                                                   caaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATgg                                              <  2:1596395/100‑1 (MQ=255)                                                   caaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATgg                                              <  2:991081/100‑1 (MQ=255)                                                    aaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATgga                                             <  1:1052412/100‑2 (MQ=255)                                                      tGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCt                                           <  2:933219/100‑1 (MQ=255)                                                      tGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCt                                           <  2:1679005/100‑1 (MQ=255)                                                      tGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCt                                           <  1:385552/100‑1 (MQ=255)                                                       gCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTg                                          <  2:1777833/100‑1 (MQ=255)                                                        cGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGa                                         >  1:270634/1‑100 (MQ=255)                                                        cGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCATCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCt                                           <  1:1312465/98‑1 (MQ=255)                                                         gtgtGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGaa                                        >  2:1336921/1‑100 (MQ=255)                                                          tgtgGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTCGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAat                                       <  1:1224095/100‑1 (MQ=255)                                                                tATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGGAGTGGTGACCAATGGTCTGAATATCGcc                                 >  2:1782685/1‑100 (MQ=255)                                                                 aTTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCg                                <  2:248804/100‑1 (MQ=255)                                                                  ntCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCg                                >  2:66989/2‑99 (MQ=255)                                                                   tCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGt                              <  1:355493/100‑1 (MQ=255)                                                                    ccGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGt                              >  2:279844/1‑99 (MQ=255)                                                                    ccGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTg                             <  2:1312745/100‑1 (MQ=255)                                                                     cGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTgg                            <  2:371713/100‑1 (MQ=255)                                                                        ccGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCAt                         <  1:653685/100‑1 (MQ=255)                                                                              tCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCg                    <  1:1082980/99‑1 (MQ=255)                                                                                  tGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCgtggtg               <  1:14489/100‑1 (MQ=255)                                                                                   gcgcTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGtggtgg              <  2:1414597/100‑1 (MQ=255)                                                                                    cgcTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTggtggt             <  2:1781903/100‑1 (MQ=255)                                                                                      ctgtctgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttg           <  1:1752165/100‑1 (MQ=255)                                                                                       tgtctgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttgg          <  2:96899/100‑1 (MQ=255)                                                                                       tgtctgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttgg          <  2:1139453/100‑1 (MQ=255)                                                                                        gtctgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttggt         <  1:571806/100‑1 (MQ=255)                                                                                          ctgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTa       <  2:552464/100‑1 (MQ=255)                                                                                           tgtTGGTGCCAGCGATGTACAGAACATGCTGAATTCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCTTGGTGGTTGGTTa       <  2:247728/99‑1 (MQ=255)                                                                                           tgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTAt      >  2:1069591/1‑100 (MQ=255)                                                                                            gtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATg     <  1:1167791/100‑1 (MQ=255)                                                                                             ttGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTAtcc    <  2:1228452/100‑3 (MQ=255)                                                                                              tGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCg   >  1:1347881/1‑100 (MQ=255)                                                                                              tGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCg   >  1:550623/1‑100 (MQ=255)                                                                                               ggTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGGGGCATGATCGTGGTGGTTGGTTATGCGa  >  1:1267800/1‑100 (MQ=255)                                                                                                  |                                                                                                 CAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGA  >  NC_000913/1903474‑1903667

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑