Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,411	+C	coding (494/516 nt)	b4555 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,410	1	.	C	100.0%	242.4 / NA	77	A165P (GCT→CCT)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (35/42);  total (35/42)

TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GC‑TGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATGGGCAGTGGC  >  NC_000913/4008346‑4008492                                                                          |                                                                                        tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     <  1:4432993/93‑1 (MQ=255) tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     <  1:2592961/93‑1 (MQ=255) tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     >  2:3254248/1‑93 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg                                                                   <  1:3793677/93‑3 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg                                                                   <  1:3632859/93‑3 (MQ=255)    ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg                                                                  >  1:1240529/1‑90 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttggt                                                                 <  1:1051163/93‑5 (MQ=255)     gAAGTGATGGCGGGCGGCGGTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttggt                                                                 >  1:3702178/1‑89 (MQ=255)           aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                           <  2:229684/93‑1 (MQ=255)           aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                           <  2:760103/93‑1 (MQ=255)           aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                           >  2:1077404/1‑93 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  1:1566229/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  1:1894017/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  1:3374702/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                         <  1:401856/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAG‑CCGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                         <  2:3408020/93‑1 (MQ=255)              gcgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATg                                                        <  2:1467147/93‑1 (MQ=255)              gcgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATg                                                        <  1:3117785/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                                      <  1:4425676/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                                      <  1:1119358/93‑1 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacg                                                    >  1:4457103/1‑93 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                                   >  1:4576177/1‑93 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                                   <  2:3526130/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                                  <  1:2958163/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                                  <  2:4322943/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                                  >  2:516542/1‑93 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                                  >  2:4523682/1‑93 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                                  <  1:2669860/93‑1 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgggg                                                 >  1:2074904/1‑90 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                                 >  2:2058391/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                <  2:1382101/93‑1 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                <  1:1265185/93‑1 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                >  1:2192640/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                >  2:4150932/1‑93 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                               <  2:1470272/93‑1 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                               >  2:1671891/1‑93 (MQ=255)                       gTTTCAAAAGGCCATGCGCAGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                               >  2:4571105/1‑93 (MQ=255)                           canaaGNNCATGCGCTGGAAG‑NNGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           <  1:4559497/90‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           <  2:3847674/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           <  1:2234580/91‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:4466518/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          <  2:4362651/92‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  2:1013108/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:2475525/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:2030356/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  2:2669759/2‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATg                                         >  1:1050044/1‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATg                                         >  1:4590471/1‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATg                                         >  2:470735/1‑93 (MQ=255)                              aaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                                        <  2:1078745/93‑1 (MQ=255)                              aaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                                        <  1:4450069/93‑1 (MQ=255)                              aaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                                        >  1:3864513/1‑93 (MQ=255)                              aaGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                                        <  1:2907437/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  1:4631955/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  2:2559408/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  1:3115899/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       >  1:4654945/1‑93 (MQ=255)                               aGGCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       >  2:1507239/1‑93 (MQ=255)                                ggCCATGCGCTGGAAGCGG‑TGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                                      <  2:3964472/93‑1 (MQ=255)                                                               ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  2:2551572/90‑1 (MQ=255)                                                               ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  2:2827746/4‑93 (MQ=255)                                                                tgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       <  1:3975408/91‑1 (MQ=255)                                                                tgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       >  1:1030894/3‑93 (MQ=255)                                                                 gggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      <  2:826713/92‑1 (MQ=255)                                                                 gggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      <  2:483481/92‑1 (MQ=255)                                                                 gggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      <  2:4494890/92‑1 (MQ=255)                                                                 gggCTACAGCCTGAAGGATTGTATTGCGTTTGGCGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      >  2:4215796/2‑93 (MQ=255)                                                                  ggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     >  2:3217413/1‑93 (MQ=255)                                                                  ggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     <  1:2506546/93‑1 (MQ=255)                                                                  ggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     >  2:2396445/1‑93 (MQ=255)                                                                    cTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   <  2:2953294/93‑2 (MQ=255)                                                                    cTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   <  1:3340585/93‑2 (MQ=255)                                                                    cTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   >  1:2035757/1‑92 (MQ=255)                                                                     tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:689379/1‑91 (MQ=255)                                                                     tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  2:2696585/1‑91 (MQ=255)                                                                     tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:1686572/1‑91 (MQ=255)                                                                     tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  2:2407127/1‑91 (MQ=255)                                                                          |                                                                                        TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GC‑TGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATGGGCAGTGGC  >  NC_000913/4008346‑4008492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑