Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,655,775	G→A	S431F (TCT→TTT)	secY ←	preprotein translocase subunit SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,655,775	0	G	A	100.0%	226.2 / NA	68	S431F (TCT→TTT)	secY	preprotein translocase subunit SecY
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (12/56);  total (12/56)

CGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAA  >  NC_017635/3655728‑3655820                                                |                                              cGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAc                                             <  1:1952464/50‑1 (MQ=255) cGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAc                                             <  2:2000178/50‑1 (MQ=255) cGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAAc                                             <  2:1860164/50‑1 (MQ=255)  gACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACt                                            <  1:1010827/50‑1 (MQ=255)  gACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACt                                            >  2:144920/1‑50 (MQ=255)   aCCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTc                                           <  1:273713/50‑1 (MQ=255)    ccAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCa                                          <  1:1242117/50‑1 (MQ=255)    ccAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCa                                          <  1:1253501/50‑1 (MQ=255)    ccAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCa                                          <  1:942855/50‑1 (MQ=255)     cAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCa                                          >  2:740377/1‑49 (MQ=255)     cAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCAt                                         <  2:1511250/50‑1 (MQ=255)       aTTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATac                                       <  1:927148/50‑1 (MQ=255)        ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATact                                      <  2:727383/50‑1 (MQ=255)        ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATact                                      <  2:1906565/50‑1 (MQ=255)        ttATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATact                                      <  1:291388/50‑1 (MQ=255)         tATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATact                                      >  2:1091852/1‑49 (MQ=255)          aTCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactg                                     <  1:836253/49‑1 (MQ=255)           tCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgac                                   <  2:566232/50‑1 (MQ=255)            cGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgact                                  >  2:703640/1‑50 (MQ=255)            cGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgact                                  >  1:48328/1‑50 (MQ=255)             ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgactg                                 <  2:1250162/50‑1 (MQ=255)             ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgactg                                 >  1:362761/1‑50 (MQ=255)             ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgactg                                 <  1:7694/50‑1 (MQ=255)             ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgactg                                 <  1:1062486/50‑1 (MQ=255)             ggCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATactgactg                                 <  1:1436063/50‑1 (MQ=255)               ccGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGa                               <  1:28792/50‑1 (MQ=255)               ccGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGa                               >  1:1561333/1‑50 (MQ=255)                cGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGa                               >  1:1965886/1‑49 (MQ=255)                cGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACCGACTGGAc                              <  1:1129199/50‑1 (MQ=39)                 gTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAca                             <  2:357557/50‑1 (MQ=255)                 gTAGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAca                             <  1:1332168/50‑1 (MQ=255)                   aGCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAcat                            >  2:1704626/1‑49 (MQ=255)                    gCCTTTCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGAcatca                          <  2:932628/50‑1 (MQ=255)                         tCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAtcatca                       <  1:1605316/48‑1 (MQ=255)                         tCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAtcatca                       <  2:305215/48‑1 (MQ=255)                         tCAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACAtcatca                       <  1:1130845/48‑1 (MQ=255)                          cAGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCaga                     <  2:141551/49‑1 (MQ=255)                           aGGTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGt                   <  1:336790/50‑1 (MQ=255)                            ggTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGtt                  <  2:253145/50‑1 (MQ=255)                             gTTCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGttt                 <  2:350461/50‑1 (MQ=255)                              ttCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTg                <  1:1020845/50‑1 (MQ=255)                              ttCGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTg                <  2:1612839/50‑1 (MQ=255)                                cGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGc               <  1:754398/49‑1 (MQ=255)                                cGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGc               <  2:1734426/49‑1 (MQ=255)                                cGCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCa              >  1:764267/1‑50 (MQ=255)                                 gCCTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCAc             <  1:877906/50‑1 (MQ=255)                                  ccTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACt            >  2:584188/1‑50 (MQ=255)                                  ccTTCTTCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACt            <  2:1401464/50‑1 (MQ=255)                                   cttcttCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACtt           <  2:496992/50‑1 (MQ=255)                                   cttcttCAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACtt           <  1:1866373/50‑1 (MQ=255)                                   cttcttCAACGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACtt           <  1:1489469/50‑1 (MQ=255)                                      cttcAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTg          <  1:715820/48‑1 (MQ=255)                                      cttcAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTg          <  2:1985388/48‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAg        <  1:595645/47‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAg        <  1:1296488/47‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  2:2025231/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  1:628981/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  1:1838153/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  2:1643361/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  1:1469246/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  2:1219185/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  1:1386416/49‑1 (MQ=255)                                         cAATGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGcc      <  2:1405021/49‑1 (MQ=255)                                          aaTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCa     <  1:1936429/49‑1 (MQ=255)                                           aTGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCAt    >  2:1976742/1‑49 (MQ=255)                                            tGCAAACTCATACTGACTGGACATCATCAGAGTTTGCat             <  1:817043/39‑2 (MQ=39)                                            tGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATaa  <  1:1426669/50‑1 (MQ=255)                                            tGCAAACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATaa  <  1:1341011/50‑1 (MQ=255)                                                |                                              CGACCAATTATCGGCCGTAGCCTTTCAGGTTCGCCTTCTTCAATGCAGACTCATACTGACTGGACATCATCAGAGTTTGCACTTGAGCCATAA  >  NC_017635/3655728‑3655820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑