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%	258.4 / NA	72	A165P (GCT→CCT)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (29/43);  total (29/43)

TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATGGGCAGTGGC  >  NC_000913/4008346‑4008492                                                                         |                                                                                        tCTGGAAGTGATGGCGGGCGGCGTTTCAAAATGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     <  1:1901182/93‑1 (MQ=255) tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     >  2:3190494/1‑93 (MQ=255) tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtt                                                                     <  2:2842303/93‑1 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGttt                                                                    <  1:4465851/93‑2 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGttt                                                                    <  1:2334120/93‑2 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg                                                                   <  1:1737083/93‑3 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg                                                                   <  1:4989388/93‑3 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttggt                                                                 <  2:6069960/93‑5 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttggt                                                                 <  1:4817457/93‑5 (MQ=255)     gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttggt                                                                 <  2:226086/93‑5 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  1:2302993/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  2:2950850/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                          <  2:4924566/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                         <  2:2143856/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                         <  2:743236/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                         <  1:1022573/93‑1 (MQ=255)               ggggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGa                                                       <  2:3840682/92‑1 (MQ=255)               cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGa                                                       <  2:3318504/93‑1 (MQ=255)               cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGa                                                       <  1:1615914/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                                      >  1:3361384/1‑93 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                                      <  2:1588234/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                                     <  1:2267000/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                                     <  2:4580266/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                                     <  2:4815600/93‑1 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGCTTGTATTGCGTTTGGTGACGGGATGAacg                                                    >  2:4396292/1‑93 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacg                                                    <  2:4018872/93‑1 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacg                                                    <  2:2466906/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                                   <  2:4254565/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                                   <  2:670750/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                                   <  1:4477690/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAGGAacga                                                   <  1:5107890/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGTGTTTGGTGACGGGAGGAacgac                                                  >  2:2158791/1‑93 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                                 >  1:3018123/1‑93 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                                 >  2:2336717/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                >  2:3055681/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                                <  1:4718515/93‑1 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                               <  2:6070951/93‑1 (MQ=255)                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaa                                            >  2:1177485/4‑93 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           <  1:3624707/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           <  1:824842/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                           >  2:4662578/3‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  2:4072808/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          <  1:2804031/92‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:1681157/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  2:2985712/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  2:4803706/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:5024781/2‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAtc                                         >  2:4531756/1‑92 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATg                                         >  2:662695/1‑93 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  2:4274699/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  2:910103/93‑1 (MQ=255)                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                                      >  2:5616454/1‑93 (MQ=255)                                                             actgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         >  2:1792161/5‑93 (MQ=255)                                                              ctgtgCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  1:382962/89‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  2:3723597/90‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  1:3063491/90‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  1:966505/4‑93 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  1:383176/90‑1 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  2:4734852/4‑93 (MQ=255)                                                              ctgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  1:5705746/4‑93 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       >  1:3351464/3‑93 (MQ=255)                                                               tgggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       >  1:919547/3‑93 (MQ=255)                                                                gggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      <  2:3709804/92‑1 (MQ=255)                                                                 ggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     <  2:1310687/93‑1 (MQ=255)                                                                 ggCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     <  1:1253718/93‑1 (MQ=255)                                                                  gCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    >  1:5812511/1‑93 (MQ=255)                                                                  gCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    >  1:5812512/1‑93 (MQ=255)                                                                  gCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    <  2:3612738/93‑1 (MQ=255)                                                                   cTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   >  1:5478868/1‑92 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:730087/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:3730112/1‑91 (MQ=255)                                                                    tACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:3412077/1‑91 (MQ=255)                                                                         |                                                                                        TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑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 < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑