Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,421	+T	coding (504/516 nt)	b4555 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,421	1	.	T	100.0%	249.1 / NA	71	L168F (TTG→TTT)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (40/31);  total (40/31)

TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCG‑TT‑‑G‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑C‑GGGAAA‑GCTGCATTATGGGCAGTGGCCACCAGCGTCT  >  NC_000913/4008346‑4008503                                                                                     |                                                                                          tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tt                                                                                  <  2:1756261/93‑1 (MQ=255)  gtGGAAGTGATGGCGGGCGGCGTGTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑ttt                                                                                 <  2:1612774/92‑2 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑ttt                                                                                 <  2:2585349/93‑2 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tttg                                                                                >  1:3760002/1‑91 (MQ=255)    ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tttgg                                                                               >  1:1504553/1‑90 (MQ=255)    ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tttgg                                                                               >  1:4328546/1‑90 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tttggt                                                                              <  2:3225814/93‑5 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑tttggt                                                                              >  2:362797/1‑89 (MQ=255)           gtGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACggg                                                                       <  1:3290333/92‑1 (MQ=255)           aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACggg                                                                       <  1:980410/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCAATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGa                                                                      <  2:2605564/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGAt                                                                     <  2:1250992/93‑1 (MQ=255)              gcgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATg                                                                    >  2:4734727/1‑93 (MQ=255)               cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGa                                                                   <  2:1009336/93‑1 (MQ=255)               cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGa                                                                   <  2:2641560/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGaa                                                                  <  1:1004691/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGaa                                                                  <  2:594135/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAac                                                                 >  2:2025077/1‑93 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTAGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAac                                                                 >  2:1242468/1‑93 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacg                                                                <  1:3802206/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacga                                                               <  1:2414018/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacgac                                                              <  1:321200/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacgac                                                              <  2:907022/93‑1 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacgacg                                                             >  1:1848270/1‑93 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAacgacg                                                             >  1:978131/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGc                                                            <  2:1666186/93‑1 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGcc                                                           >  1:1095282/1‑93 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGcc                                                           <  2:4673438/93‑1 (MQ=255)                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGaa                                                        >  2:3850580/4‑93 (MQ=255)                          gcaaaaGGCCCTGCGCTGTAAGCGCTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGaa                                                        <  2:3861309/90‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGaaa                                                       >  1:2116878/3‑93 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGaaa                                                       <  2:643823/91‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTT‑‑GTTGACGGGAGGAACTACGCCGAAAt                                                      >  2:3805337/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAAt                                                      <  2:2079373/92‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAAt                                                      >  2:208377/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAAt                                                      >  2:2436174/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAAt                                                      <  1:3137890/92‑1 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATg                                                     >  2:991364/1‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATg                                                     >  1:3644293/1‑93 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCt                                                   >  1:1869543/1‑93 (MQ=255)                                                             actgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATggg                    >  1:1016550/5‑93 (MQ=255)                                                             actgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATggg                    <  1:267191/89‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGc                   >  2:4612409/4‑93 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGc                   <  1:3744933/90‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATAATgcgc                   >  1:4680336/4‑93 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCa                  >  1:2286020/3‑93 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCa                  <  2:1794732/91‑1 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCa                  >  1:665597/3‑93 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCa                  <  1:4711744/91‑1 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCa                  >  2:2364535/3‑93 (MQ=255)                                                                gggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAg                 >  2:62315/2‑93 (MQ=255)                                                                 ggCTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGt                <  1:1646592/93‑1 (MQ=255)                                                                   cTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTgc              <  1:381191/93‑2 (MQ=255)                                                                   cTACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTgc              <  1:381190/93‑2 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGGAG‑GGGAAAGGCTGCATTATGGGCAGTgcg             >  2:970755/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAATGCTGCATTATGGGCAGTgcg             >  1:3704512/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTgcg             >  2:1579815/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTgcg             >  1:59826/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGAAGTgcg             >  1:1825793/1‑91 (MQ=255)                                                                        gccTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCgcacc         >  1:1272301/3‑93 (MQ=255)                                                                        gccTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCgcacc         >  2:2489388/3‑93 (MQ=255)                                                                        g‑CTGAAAGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCgcacca        <  1:2170429/93‑1 (MQ=255)                                                                          cTGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAg       >  2:4601069/1‑93 (MQ=255)                                                                          cTGAAGGATTGTATTGCG‑TTCGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAg       >  2:4601068/1‑93 (MQ=255)                                                                           tGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc      >  1:1685417/1‑93 (MQ=255)                                                                           tGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc      <  1:963472/93‑1 (MQ=255)                                                                           tGAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGc      >  2:1165742/1‑93 (MQ=255)                                                                            gAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCg     >  2:1517882/1‑93 (MQ=255)                                                                            gAAGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCg     >  2:3491886/1‑93 (MQ=255)                                                                              aGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGTc   >  1:253634/1‑93 (MQ=255)                                                                              aGGATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGTc   <  1:3598158/93‑1 (MQ=255)                                                                               ggATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGTCt  >  2:3354691/1‑93 (MQ=255)                                                                               ggATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGTCt  >  2:2878223/1‑93 (MQ=255)                                                                               ggATTGTATTGCG‑TTTGG‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑CGGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGCGTCt  <  1:3876459/93‑1 (MQ=255)                                                                                     |                                                                                          TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCG‑TT‑‑G‑TGACGGGATGAACGACGCCGAAATGCTGTCGATGG‑C‑GGGAAA‑GCTGCATTATGGGCAGTGGCCACCAGCGTCT  >  NC_000913/4008346‑4008503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑