Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,311,878	G→A	P252L (CCG→CTG)	truB ←	tRNA pseudouridine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,311,878	0	G	A	100.0%	272.5 / NA	89	P252L (CCG→CTG)	truB	tRNA pseudouridine synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/54);  total (35/54)

CACCAGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTGGAATAT  >  W3110S.gb/3311810‑3311944                                                                     |                                                                   cACCAGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGa                                                                  <  1:2644898/71‑1 (MQ=255) cACCAGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGa                                                                  <  1:1994127/71‑1 (MQ=255) cACCAGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGa                                                                  <  1:1823800/71‑1 (MQ=255)     aGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGt                                                              >  1:3840761/1‑71 (MQ=255)        tGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTcc                                                            >  1:2165784/1‑70 (MQ=255)        tGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTcc                                                            >  1:212211/1‑70 (MQ=255)         gTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCg                                                           >  1:3541647/1‑70 (MQ=255)         gTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCg                                                           >  1:3776267/1‑70 (MQ=255)         gTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCg                                                           >  1:2219033/1‑70 (MQ=255)          tACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGa                                                                  <  1:3417081/62‑1 (MQ=255)            cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc                                                       >  1:1971126/1‑71 (MQ=255)            cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc                                                       >  1:4084958/1‑71 (MQ=255)              aaCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGa                                                                  <  1:2265945/58‑1 (MQ=255)              aaCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg                                                     <  1:1127499/71‑1 (MQ=255)               aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg                                                    <  1:3144942/71‑1 (MQ=255)               aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg                                                    <  1:742177/71‑1 (MQ=255)               aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg                                                    <  1:24174/71‑1 (MQ=255)                 cGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGAc                                                  >  1:1413586/1‑71 (MQ=255)                  gggTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGaa                                                         <  1:3638035/63‑1 (MQ=255)                  gggTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGaa                                                         <  1:3643453/63‑1 (MQ=255)                    gTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg                                                    <  1:802264/66‑1 (MQ=255)                     ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:2895718/71‑1 (MQ=255)                     ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:347769/71‑1 (MQ=255)                     ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:4227490/71‑1 (MQ=255)                     ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:545128/71‑1 (MQ=255)                     ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:843459/71‑1 (MQ=255)                       aCCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCa                                            >  1:705946/1‑71 (MQ=255)                           tttttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg                                                     <  1:3367412/58‑1 (MQ=255)                           tttttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTgg                                        <  1:2765228/71‑1 (MQ=255)                             tttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGa                                                   >  1:3313565/1‑58 (MQ=255)                             tttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCa                                      >  1:2116650/1‑71 (MQ=255)                             tttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCa                                      >  1:1548780/1‑71 (MQ=255)                             tttGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCa                                      >  1:3732701/1‑71 (MQ=255)                                gAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATc                                    <  1:646616/70‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCatt                                 <  1:4023390/71‑3 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:27549/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:3732678/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:1286148/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:1352085/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:928025/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:4481846/71‑1 (MQ=255)                                  aGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:524352/71‑1 (MQ=255)                                   gTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg                                                     <  1:3641346/50‑1 (MQ=255)                                   gTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:2955647/70‑1 (MQ=255)                                    tAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:3965371/56‑1 (MQ=255)                                    tAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:4112700/56‑1 (MQ=255)                                    tAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTgg                                        <  1:2857041/62‑1 (MQ=255)                                    tAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTgg                                        <  1:319522/62‑1 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGAc                                                  >  1:954957/1‑50 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGAc                                                  >  1:2662918/1‑50 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:2209031/54‑1 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTgg                                        >  1:843543/1‑60 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTgg                                        >  1:456617/1‑60 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCa                                   >  1:4112524/1‑65 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTaa                               >  1:3154107/1‑69 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             >  1:3479985/1‑71 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             <  1:822483/71‑1 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             >  1:1565464/1‑71 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             >  1:1855170/1‑71 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             >  1:4220949/1‑71 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg                             <  1:4034974/71‑1 (MQ=255)                                      aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCAGAAGCTGGACTGTCCa                                            >  1:32987/1‑56 (MQ=255)                                            agaCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg                                                    <  1:4358326/42‑1 (MQ=255)                                            agaCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTa                                >  1:1681344/1‑62 (MQ=255)                                            agaCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATc                         >  1:320547/1‑69 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:3473580/71‑1 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:1446217/71‑1 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:2149656/71‑1 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:2926443/71‑1 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:196688/71‑1 (MQ=255)                                              aCGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:283776/71‑1 (MQ=255)                                               cGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:1076662/70‑1 (MQ=255)                                               cGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:3656962/70‑1 (MQ=255)                                                ggtAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTcc                                             <  1:3853429/43‑1 (MQ=39)                                                gTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTaa                   >  1:1001279/1‑71 (MQ=255)                                                 ttAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:2524760/56‑1 (MQ=255)                                                 ttAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:1573144/68‑1 (MQ=255)                                                   aaCGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAAt                              >  1:844552/1‑57 (MQ=255)                                                   aaCGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTaa                   >  1:237235/1‑68 (MQ=255)                                                       gAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTc                                              <  1:1967616/37‑1 (MQ=255)                                                       gAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTaa                   >  1:3663764/1‑64 (MQ=255)                                                       gAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCcgcg            <  1:3869675/71‑1 (MQ=255)                                                       gAAGATTCACCACCAGATAGTCCGAAGCAGGACTCTCCATAGGCATCAGTAATGGATCAAGTaa                   >  1:3519835/1‑64 (MQ=255)                                                         aGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTaa                               >  1:1624186/1‑50 (MQ=255)                                                          gATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt                     <  1:1667441/59‑1 (MQ=255)                                                             tCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTgg       >  1:355976/1‑70 (MQ=255)                                                              caccacCAGATAGTCCGATGCTGGACTGTCCATTg                                         >  1:2019101/1‑35 (MQ=38)                                                                ccaccaGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTaa                               >  1:4114347/1‑43 (MQ=255)                                                                ccaccaGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTGGAata   <  1:929159/71‑1 (MQ=255)                                                                ccaccaGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTGGAata   <  1:2487755/71‑1 (MQ=255)                                                                ccaccaGATAGTCCGAAGCAGGACTGTCCATTGGCATCAGTa                                >  1:4108925/1‑42 (MQ=255)                                                                 caccAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTGGAatat  <  1:643927/71‑1 (MQ=255)                                                                  accAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt                                 <  1:1088230/39‑1 (MQ=255)                                                                     |                                                                   CACCAGATGTACGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGTAACTCCGCGGCTGGAATAT  >  W3110S.gb/3311810‑3311944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑