Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,903,571	A→G	36.6%	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	36.6%	50.8 / 72.6	74	T164A (ACC→GCC)	manY	mannose‑specific enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base A (19/28);  new base G (10/17);  total (29/45)
Fisher's exact test for biased strand distribution p-value = 8.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.72e-01

GCAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGATG  >  NC_000913/1903473‑1903669                                                                                                   |                                                                                                   gCAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTAc                                                                                                   <  2:852146/100‑1 (MQ=255)  cAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGcc                                                                                                  <  1:1017617/100‑1 (MQ=255)  cAACCTGACAGCGATTTCCTGGATCCACGCTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATCCCGGCCGTCATCGTTGCGCTGTCTGTTGGTAcc                                                                                                  <  2:1347780/100‑1 (MQ=255)     ccTGACAGCGATTTCCTGGATCCACGTTTCGTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAg                                                                                                <  1:211987/99‑1 (MQ=255)      cTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCg                                                                                              >  1:1610979/1‑100 (MQ=255)      cTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCg                                                                                              >  1:1609314/1‑100 (MQ=255)         aCAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAg                                                                                           <  1:51605/100‑1 (MQ=255)         aCAGCGATTTCCTGGATCCACGTTTCATCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAg                                                                                           <  2:1507669/100‑1 (MQ=255)          cAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGt                                                                                          >  2:951442/1‑100 (MQ=255)          cAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGt                                                                                          <  1:651459/100‑1 (MQ=255)            gCGATTTCCTGTATCCACGTTTCTTCTCTGTGCCTGCAAGCAATGCGTGTGGCTAGTCCGGCAGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTa                                                                                         <  2:2080735/99‑1 (MQ=255)             cGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACa                                                                                       <  1:476749/100‑1 (MQ=255)               aTTTCCTGGATCTACGTTTCTTTTCTGTTGCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACa                                                                                       <  1:481805/98‑1 (MQ=255)               aTTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGa                                                                                     <  2:1071988/100‑1 (MQ=255)               aTTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGa                                                                                     >  2:1597242/1‑100 (MQ=255)                  tCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACa                                                                                  <  2:1803687/100‑1 (MQ=255)                  tCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACa                                                                                  >  2:1639915/1‑100 (MQ=255)                  tCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTCGGTGCCAGCGAAGTACAGAACa                                                                                  <  1:1994724/100‑1 (MQ=255)                    cTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATg                                                                                <  2:1970086/100‑1 (MQ=255)                     tGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGc                                                                               <  1:981791/100‑1 (MQ=255)                       gATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTg                                                                             >  1:2125525/1‑100 (MQ=255)                       gATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCt                                                                              <  1:211176/99‑1 (MQ=255)                           cACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATg                                                                         <  2:942992/100‑1 (MQ=255)                                  cttctCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTcc                                                                  <  1:1569899/100‑1 (MQ=255)                                  cttctCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTcc                                                                  <  2:1495004/100‑1 (MQ=255)                                  cttctCGGTTCCTGCAAGCAAGGGGTGTGGCTATTCCGGCCGTAATCGTTGCGCTGTCTGTTGGGACCAGCTGAGGACAGAACAAGCAGAATga                                                                        <  2:136998/94‑2 (MQ=255)                                    tctcTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCgg                                                                <  1:69550/100‑1 (MQ=255)                                     ctctGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGa                                                               <  2:912059/100‑1 (MQ=255)                                        ttttCCTGCAAGCAATTCGTGTGCCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAg                                                             <  1:1821375/97‑1 (MQ=255)                                        tGTTCCTGCAAGCCATGCGTGTAGATATTCCGGCCGTCATCGTTGCGATGTCTGTTGGTACCAGCGAATTACAGATCATGTTGTATGGGATTCCGGAAgt                                                            <  2:1413280/100‑1 (MQ=255)                                         gTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtg                                                           <  1:511944/100‑1 (MQ=255)                                           tCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggt                                                         >  1:2233816/1‑100 (MQ=255)                                            ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                        >  2:587525/1‑100 (MQ=255)                                            ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                        >  1:515427/1‑100 (MQ=255)                                            ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                        >  1:719826/1‑100 (MQ=255)                                            ccTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAgtggtg                                                        <  1:1132944/100‑1 (MQ=255)                                             cTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGa                                                       >  1:2248101/1‑100 (MQ=255)                                              tGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAc                                                      >  1:87546/1‑100 (MQ=255)                                              tGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGCAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAc                                                      >  1:2195320/1‑100 (MQ=255)                                              tGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAc                                                      <  1:1798272/100‑1 (MQ=255)                                              tGCAAGCAATGCGTGTGGCTAATCCGGCCGTCATCGATGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAc                                                      >  2:664668/1‑100 (MQ=255)                                               gcaagcaaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAcc                                                     <  1:143092/100‑1 (MQ=255)                                               gcaagcaaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGAcc                                                     >  2:1001677/1‑100 (MQ=255)                                                caagcaaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCa                                                    >  2:126996/1‑100 (MQ=255)                                                    caaTGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATgg                                                <  2:1801541/100‑1 (MQ=255)                                                        gCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTg                                            <  2:1943013/100‑1 (MQ=255)                                                          gtgtGGCTATTCCGGGCGTCATCGTTGCGCTGTCTGTTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGaa                                          <  1:2215835/100‑1 (MQ=255)                                                            gtgGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAata                                        <  2:1145084/100‑1 (MQ=255)                                                            gtgGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAata                                        >  2:301576/1‑100 (MQ=255)                                                            gtgGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGACTGAata                                        >  1:1231491/1‑100 (MQ=255)                                                              ggCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAata                                        >  1:1564953/1‑98 (MQ=255)                                                              ggCTATTCCGGCCATCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCTGAAGTGGTGAGCAATGGTCTGAatat                                       >  2:195660/1‑99 (MQ=255)                                                               gCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCg                                     <  1:1627451/100‑1 (MQ=255)                                                                       ggCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGGGGTGACCAATGGTCTGAATATCGCCGGTGGc                             >  1:1565958/1‑100 (MQ=255)                                                                          cGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATg                          <  1:1331276/100‑1 (MQ=255)                                                                           gTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGa                         >  2:1742912/1‑100 (MQ=255)                                                                             cATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATc                       >  2:1703580/1‑100 (MQ=255)                                                                              aTCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCg                      <  2:900007/100‑1 (MQ=255)                                                                                      gcTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggtt              <  1:2143585/100‑1 (MQ=255)                                                                                       ctgtctgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttg             <  1:1857280/100‑1 (MQ=255)                                                                                        tgtctgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttgg            <  2:238719/100‑1 (MQ=255)                                                                                        tgtctgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttgg            <  1:1001679/100‑1 (MQ=255)                                                                                         gtctgtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGtggttggt           <  1:1679335/100‑1 (MQ=255)                                                                                           ctgtTGGTATCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTa         <  1:729549/100‑1 (MQ=255)                                                                                            tgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTAt        >  1:1187842/1‑100 (MQ=255)                                                                                            tgtTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTAt        >  1:838108/1‑100 (MQ=255)                                                                                             gtTGGTGCCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTAt        >  1:56976/1‑99 (MQ=255)                                                                                              ttGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGc      <  1:1318426/100‑1 (MQ=255)                                                                                               tGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCg     <  1:1095763/100‑1 (MQ=255)                                                                                                ggTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGa    >  1:763648/1‑100 (MQ=255)                                                                                                 gTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGAt   >  2:2121475/1‑100 (MQ=255)                                                                                                 gTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGAt   <  1:2227572/100‑1 (MQ=255)                                                                                                 gTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGAGAt   >  1:764324/1‑100 (MQ=255)                                                                                                  tACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGATg  <  2:1915727/100‑1 (MQ=255)                                                                                                   |                                                                                                   GCAACCTGACAGCGATTTCCTGGATCCACGTTTCTTCTCTGTTCCTGCAAGCAATGCGTGTGGCTATTCCGGCCGTCATCGTTGCGCTGTCTGTTGGTACCAGCGAAGTACAGAACATGCTGAATGCGATTCCGGAAGTGGTGACCAATGGTCTGAATATCGCCGGTGGCATGATCGTGGTGGTTGGTTATGCGATG  >  NC_000913/1903473‑1903669

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: ‑