Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,246,073	C→T	100%	G435D (GGC→GAC)	treA ←	periplasmic trehalase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,246,073	0	C	T	100.0%	209.2 / ‑6.7	65	G435D (GGC→GAC)	treA	periplasmic trehalase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (40/24);  minor base A (1/0);  total (41/24)

GTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGCCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGGGCGG  >  NC_000913/1245976‑1246166                                                                                                  |                                                                                              gTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGgtcg                                                                                             <  1:1368948/100‑1 (MQ=255)        tGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGtt                                                                                      >  2:962293/1‑100 (MQ=255)        tGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGtt                                                                                      <  1:354383/100‑1 (MQ=255)             tCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTgcagc                                                                                 >  1:389127/1‑100 (MQ=255)                ttCTGTCGCGACCCATTGTAACGGTGCCCATCAATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGATGTGGTGTTCAGGTCGCCGGGTTGCAGCAGa                                                                              <  2:2163071/100‑1 (MQ=255)                 tCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGAt                                                                             <  2:674762/100‑1 (MQ=255)                  cTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGAtg                                                                            >  1:1215042/1‑100 (MQ=255)                   tGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTTACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGAtgt                                                                           >  2:892905/1‑100 (MQ=255)                    gTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGAtg                                                                            >  2:2170211/1‑98 (MQ=255)                      cgcgACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGtt                                                                        >  2:892633/1‑100 (MQ=255)                      cgcgACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGtt                                                                        >  2:2208297/1‑100 (MQ=255)                        cgACCCACTGTAACGGTGCCCAGCCATTTGGCGTATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGtttt                                                                      <  1:573212/100‑1 (MQ=255)                        cgACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGtttt                                                                      <  1:1594008/100‑1 (MQ=255)                        cgACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGtttt                                                                      <  1:1589731/100‑1 (MQ=255)                             cACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCAGTTTTCACCAAAGTAGTGATCAAGTCGCCGGGTTGCAGCAGATGTGTATtcgtcg                                                                 >  1:453994/1‑100 (MQ=255)                                  tAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTcgtcgccgtc                                                            >  2:1569165/1‑100 (MQ=255)                                   aaCGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTcgtcgccgtcg                                                           <  1:1293223/100‑1 (MQ=255)                                     cGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCgtcgccgtcgcc                                                         <  2:1728771/100‑1 (MQ=255)                                         gCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCAttt                                                     <  1:1087306/100‑1 (MQ=255)                                          cccAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGATCGCAGGGTTGCAGCAGATGTGTTTTCGTCGACGTCGCCAtttt                                                    >  1:250635/1‑100 (MQ=255)                                           ccAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTttg                                                   >  1:2220599/1‑100 (MQ=255)                                           ccAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGAAGATGTGTTTTCGTCGCCGTCGCCATTttg                                                   >  1:1045421/1‑100 (MQ=255)                                           ccAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGATCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTttg                                                   >  1:105652/1‑100 (MQ=255)                                            cAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTttg                                                   <  1:1847268/99‑1 (MQ=255)                                               ccATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTgg                                               >  2:512185/1‑100 (MQ=255)                                               ccATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTgg                                               >  1:392509/1‑100 (MQ=255)                                                 aTTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGgcg                                             <  2:410723/100‑1 (MQ=255)                                                     ggCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCACTTTGTTGGCGCGAt                                         >  1:1994686/1‑100 (MQ=255)                                                      gctcATCCCATTGTTGCCCATTTTTCTTCGACTTTGTTTTCAGGTTGTCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGa                                          <  1:772593/95‑1 (MQ=255)                                                      gcgcATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATc                                        >  1:1437823/1‑100 (MQ=255)                                                      gcgcATCCCATTGTTGCCCACTTTTCACCGACGTAGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATc                                        >  2:416705/1‑100 (MQ=255)                                                        gcATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCtt                                      >  1:2457793/1‑100 (MQ=255)                                                          aTCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTc                                    >  2:845645/1‑100 (MQ=255)                                                           tCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTTCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCg                                   <  1:1545194/100‑1 (MQ=255)                                                           tCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCg                                   <  1:1540335/100‑1 (MQ=255)                                                            cccATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGACGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGc                                  >  2:492410/1‑100 (MQ=255)                                                            cccATTGTTGCCCACTTTTCACCGACGCGGTGTTCAGGACGCAGGGTTGCAGCAGATGTGTTTTTGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGc                                  >  2:492726/1‑100 (MQ=255)                                                             ccATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGCTCTTTCGCt                                 >  2:1502905/1‑100 (MQ=255)                                                              cATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTg                                <  2:1133090/100‑1 (MQ=255)                                                                 tgttgCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTCGCGCGATCTTTtgctgc                               >  1:2638624/1‑98 (MQ=255)                                                                  gttgCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGc                            >  2:529572/1‑100 (MQ=255)                                                                  gttgCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCATTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGc                            >  1:256567/1‑100 (MQ=255)                                                                  gttgCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAAATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTg                                >  2:423902/1‑96 (MQ=255)                                                                    tgCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCAt                          <  2:2598240/100‑1 (MQ=255)                                                                     gCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCAtt                         >  1:2042458/1‑100 (MQ=255)                                                                     gCCCACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCAtt                         >  2:1999069/1‑100 (MQ=255)                                                                      cccACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTg                        >  1:1664646/1‑100 (MQ=255)                                                                       caaCTGTTCCCCGACGTGGTTTTTAGGTCGCCGGGTTGCAGCATAGGTGTTTTCGTGGCCGTCGCCATTTTGTCCGCGCGATCTTTCGCTGCAGCAATGa                       <  2:1184725/98‑1 (MQ=255)                                                                        cACTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGAc                      >  1:400178/1‑100 (MQ=255)                                                                         aCTTTTCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACg                     <  2:1684420/100‑1 (MQ=255)                                                                            tttCACCGACGTGGTGTTCAGGTCGCCTGGTTGCAGTAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTAc                  <  1:221515/100‑1 (MQ=255)                                                                            tttCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTAc                  >  2:2164876/1‑100 (MQ=255)                                                                            tttCACCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTAc                  >  2:939999/1‑100 (MQ=255)                                                                                aCCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCg              >  1:357758/1‑100 (MQ=255)                                                                                aCCGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCg              >  1:1403982/1‑100 (MQ=255)                                                                                 ccGACGTGGTGTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCgg             >  1:2469408/1‑100 (MQ=255)                                                                                       tggtgTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACa        >  1:1081496/1‑99 (MQ=255)                                                                                       tggtgTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAg       <  2:1283500/100‑1 (MQ=255)                                                                                        ggtgTTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAgg      >  2:645454/1‑100 (MQ=255)                                                                                         gtgtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAggg     >  2:2337275/1‑100 (MQ=255)                                                                                          tgtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTTGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggc    <  1:2454222/100‑1 (MQ=255)                                                                                          tgtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggc    >  2:276949/1‑100 (MQ=255)                                                                                          tgtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggc    <  1:2208324/100‑1 (MQ=255)                                                                                           gtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggcg   <  2:250633/100‑1 (MQ=255)                                                                                           gtTCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggcg   >  1:807896/1‑100 (MQ=255)                                                                                            ttCAGGTCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGggcgg  <  1:141145/100‑1 (MQ=255)                                                                                                  |                                                                                              GTAGTTTTGTAATCCTTCTGTCGCGACCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGGCCGCCGGGTTGCAGCAGATGTGTTTTCGTCGCCGTCGCCATTTTGTTGGCGCGATCTTTCGCTGCCGCATTGACGTACAGCGGGAACAGGGCGG  >  NC_000913/1245976‑1246166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑