Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,750,975	G→A	intergenic (‑108/‑504)	malP ← / → malT	maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,750,975	0	G	A	100.0%	227.2 / NA	65	intergenic (‑108/‑504)	malP/malT	maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (37/28);  total (37/28)

TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC  >  NC_017635/3750929‑3751021                                               |                                               ttGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGCGTTGCGGAGAt                                             >  2:1817172/1‑50 (MQ=255) ttGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt                                             >  1:2062032/1‑50 (MQ=255)  tGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGAt                                             >  2:1290282/1‑49 (MQ=255)   gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg                                            <  1:1076753/49‑1 (MQ=255)   gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg                                            <  1:718039/49‑1 (MQ=255)   gACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATg                                            <  1:644590/49‑1 (MQ=255)    aCCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGTGTTGCGGAGATGAg                                          >  2:954424/1‑50 (MQ=255)      cTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa                                        <  1:1096196/50‑1 (MQ=255)      cTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa                                        <  1:55746/50‑1 (MQ=255)      cTTCCTAATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCa                                        <  2:1403390/50‑1 (MQ=255)        tCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg                                      >  2:789340/1‑50 (MQ=255)        tCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg                                      >  1:1963131/1‑50 (MQ=255)         ccTCATCCTGCGGGGGATTAGGCAGGGAGGGGTTGCGGAGATGAGCAAg                                      >  2:1435728/1‑49 (MQ=255)         ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCaa                                       <  1:103292/48‑1 (MQ=255)         ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg                                      >  2:266783/1‑49 (MQ=255)         ccTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAg                                      >  1:1863721/1‑49 (MQ=255)          cTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAgg                                     >  2:245936/1‑49 (MQ=255)          cTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAgg                                     <  2:1021393/49‑1 (MQ=255)           tCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGa                                    >  1:329590/1‑49 (MQ=255)             aTCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAt                                 >  1:327467/1‑50 (MQ=255)             aTCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAt                                 <  1:1230419/50‑1 (MQ=255)              tCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtg                                >  1:1470872/1‑50 (MQ=255)              tCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtg                                >  2:703606/1‑50 (MQ=255)               ccTGCGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAAtgt                               >  2:1842650/1‑50 (MQ=255)                   cGGGGGATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAt                            <  1:1574655/49‑1 (MQ=255)                    gggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct                          <  2:1976423/50‑1 (MQ=255)                    gggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct                          >  2:1222908/1‑50 (MQ=255)                     ggggATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGAtct                          >  2:633113/1‑49 (MQ=255)                        gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc                      <  1:770823/50‑1 (MQ=255)                        gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc                      >  2:1917405/1‑50 (MQ=255)                        gATTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc                      <  2:844784/50‑1 (MQ=255)                         aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc                     <  2:705644/50‑1 (MQ=255)                         aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc                     <  2:495961/50‑1 (MQ=255)                         aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAcc                     <  1:1853913/50‑1 (MQ=255)                         aTTAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAAc                      >  1:1969135/1‑49 (MQ=255)                           tAGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCAc                   >  2:386198/1‑50 (MQ=255)                            aGGCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCAc                   <  1:35771/49‑1 (MQ=255)                             ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACtt                 <  1:724230/50‑1 (MQ=255)                             ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt                  <  2:2067047/49‑1 (MQ=255)                             ggCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACt                  >  1:15373/1‑49 (MQ=255)                              gCAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACtt                 >  2:935253/1‑49 (MQ=255)                               cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTaa               <  1:1343091/50‑1 (MQ=255)                               cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  1:130307/1‑49 (MQ=255)                               cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  1:530466/1‑49 (MQ=255)                               cAGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  1:1155322/1‑49 (MQ=255)                                aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTaaa              <  2:570199/50‑1 (MQ=255)                                aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  1:570144/1‑48 (MQ=255)                                aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  2:1136270/1‑48 (MQ=255)                                aGGGAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTa                >  1:833906/1‑48 (MQ=255)                                 gggAGGAGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAg             >  1:717226/1‑50 (MQ=255)                                  ggaggaGTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc            <  1:1031226/50‑1 (MQ=255)                                   gaggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc            >  2:1135107/1‑49 (MQ=255)                                    aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGc            >  1:1984052/1‑48 (MQ=255)                                    aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTa          <  2:2081530/50‑1 (MQ=255)                                    aggagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTa          <  2:465715/50‑1 (MQ=255)                                      gagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGt        >  2:538667/1‑50 (MQ=255)                                      gagTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGt        <  2:1477398/50‑1 (MQ=255)                                        gTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTg       >  1:682405/1‑49 (MQ=255)                                        gTTGCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGc      <  1:1981861/50‑1 (MQ=255)                                           gCGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCaaa   >  1:2044149/1‑50 (MQ=255)                                            cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCaaa   <  2:1480557/49‑1 (MQ=255)                                            cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc  >  1:617493/1‑50 (MQ=255)                                            cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc  >  2:78788/1‑50 (MQ=255)                                            cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc  <  1:290109/50‑1 (MQ=255)                                            cGGAGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAc  >  2:866374/1‑50 (MQ=255)                                               |                                               TTGACCTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGAGTTGCGGGGATGAGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCAAAC  >  NC_017635/3750929‑3751021

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: ‑