Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,458,392	T→C	G18G (GGT→GGC)	gspE →	Type II secretion system protein GspE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,458,392	0	T	C	100.0%	102.9 / NA	32	G18G (GGT→GGC)	gspE	Type II secretion system protein GspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/20);  total (12/20)

ACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTTCTCTCGCTTTCGGAAGAGATGCCCGCAAATGAAGATCTCC  >  NC_000913/3458150‑3458636                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                     acgaTTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATctct                                                                                                                                                                                                                                               >  2:1976/1‑250 (MQ=255)      tATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACCCCCGTTACCGTCCGGAGCAACAACAGCGGATCGACGGGAAATCAAAATCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCTCTCCCC‑TTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCa                                                                                                                                                                                                                                          <  1:17453/250‑1 (MQ=255)          cGTGACGATGATGTTTATAGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAAAAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCCGAggg                                                                                                                                                                                                                                     >  1:145758/1‑251 (MQ=255)                   gatgTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGattat                                                                                                                                                                                                                            <  1:108156/251‑1 (MQ=255)                          aTCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTAtctc                                                                                                                                                                                                                     <  1:116188/251‑1 (MQ=255)                                       aaaaGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCAt                                                                                                                                                                                                        >  1:138015/1‑251 (MQ=255)                                        aaaGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCAtt                                                                                                                                                                                                       <  1:321800/251‑1 (MQ=255)                                        aaaGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCAtt                                                                                                                                                                                                       >  1:294073/1‑251 (MQ=255)                                                                           acaGCGGATCGACGGGAAATCAAAAGCGCGGGGTGGCTCGGAATATTTGCCGGGGCTGGAGGAAAACACGTTCAACAGGCCCGCCCCTGCGCCATCGTCACGGTGAGGCATTCATAGGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTGATCTCGTCGATACGCCATTCGAGCGGTTACTCGAGATTCAACGTCAGGTTGGcc                                                                                                                                                                    <  2:145758/251‑1 (MQ=255)                                                                               cGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTg                                                                                                                                                                >  1:160615/1‑251 (MQ=255)                                                                                        gggAAATCAAAAGCGCTGGTTGGCGCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGGGGCATTCAAATGAGAATTCCCTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCAt                                                                                                                                                       <  2:113842/251‑1 (MQ=255)                                                                                            aaTCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGAcc                                                                                                                                                   >  2:98564/1‑251 (MQ=255)                                                                                                        tGGTTGGCTCGGCAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTcac                                                                                                                                         >  2:121676/1‑249 (MQ=255)                                                                                                                               gTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGa                                                                                                                <  2:226299/251‑1 (MQ=255)                                                                                                                                 gCTGGATGAACACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAAGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGATGGa                                                                                                                >  2:139836/1‑249 (MQ=255)                                                                                                                                 gCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCCCTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGaa                                                                                                               <  1:112072/250‑1 (MQ=255)                                                                                                                                    tgctaaaacgccGTTCAACAGTCGTGCCCCTGGGCCATCGTCACGGTGAGGCATTCATGTGCGAATTC‑CTTACCCTTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCATAGGGCGATATTATTTATCTCGCCGATACGCCATTCGAGCGGTTTCTCGATATTCAACGTCAGTTTGGCCAGTGCAAGACCCTGACCAGCGTGGCACAGGCTGATTTTGAAGCTCGGCTGGAAg                                                                                                              <  1:359967/237‑1 (MQ=255)                                                                                                                                         aaaaCACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTc                                                                                                      >  2:303216/1‑251 (MQ=255)                                                                                                                                               cgtccAACAGTCCCCCCCCTGCACCATCGCCAGGTTGAGGAATTCAAATACGATTTAACTCCCC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTTTCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAg                                                                                                <  2:100964/247‑1 (MQ=255)                                                                                                                                               cGTTCAACAGTCACGCCCCGGCGACATCGTCACGGTGAGGCATTCATATGGGAAGTCACCCACC‑GTCCCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTGCTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAg                                                                                                <  2:100969/251‑1 (MQ=255)                                                                                                                                                 ttCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTAGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGa                                                                                               >  2:190394/1‑250 (MQ=255)                                                                                                                                                     acggtcccgtcccttcaccttcgccACGGTGAGGCATTCATATGAGTATTCGCTCCCC‑GTACCCCGCCAGTTGGGCGCTGGCACAACCAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGTCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATAcc                                                                                          <  2:283202/227‑1 (MQ=255)                                                                                                                                                      cAGTCACGCCCCCGCGCCCTCGTCAAGGTGAGGCATTCATATGAGAATTCCCTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGACTTGGCTATCTCTATTCAGAGGGCGAGCTTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGGTATTCCACGTCAGGTTGGCCAGGCCCCGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGCTATTCCATCGGAATAccc                                                                                         >  2:361129/1‑250 (MQ=255)                                                                                                                                                                              aCGGTGAGGCATTCAAATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAgg                                                                 <  2:89593/251‑1 (MQ=255)                                                                                                                                                                                ggggAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGat                                                               <  1:1976/248‑1 (MQ=255)                                                                                                                                                                                          tCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCaa                                                      <  2:294073/250‑1 (MQ=255)                                                                                                                                                                                                   agttcactaccc‑GTAGCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCGCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGAGTGCGCAGGATATGGATCAATCCGTCGAtc                                            <  2:183726/241‑1 (MQ=255)                                                                                                                                                                                                      tcactcacC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGAtctt                                          <  1:324037/250‑1 (MQ=255)                                                                                                                                                                                                           cacC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTtctct                                      <  1:108367/249‑1 (MQ=255)                                                                                                                                                                                                                gTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTTCTCTCGCttt                                >  1:159525/1‑251 (MQ=255)                                                                                                                                                                                                                             tGGGCGCTGGCACAACGAATTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTTCTCTCGCTTTCGGAAGAGATGc                    <  1:237955/250‑1 (MQ=255)                                                                                                                                                                                                                                              aaTTGGCTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTTCTCTCGCTTTCGGAAGAGATGCCCACAAATGAAGATCTcc  <  1:190394/251‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                     ACGATTATCCGTGACGATGATGTTTATCGCTCACTGTCAAAAGAGAAATACACCCGTTACCGTCAGGAGCAACAACAGCGGATCGACGGGAAATCAAAAGCGCTGGTTGGCTCGGAAGATTTGCCGGTGCTGGATGAAAACACGTTCAACAGTCACGCCCCTGCGCCATCGTCACGGTGAGGCATTCATATGAGAATTCACTCACC‑GTACCCCGCCAGTTGGGCGCTGGCACAACGAATTGGTTATCTCTATTCAGAGGGCGAGATTATTTATCTCGCCGATACGCCATTCGAGCGGTTACTCGATATTCAACGTCAGGTTGGCCAGTGCCAGACCATGACCAGCTTGTCACAGGCTGATTTTGAAGCTCGGCTGGAAGCGGTATTCCATCAGAATACCGGTGAGTCGCAACAGATTGCGCAGGATATCGATCAATCCGTCGATCTTCTCTCGCTTTCGGAAGAGATGCCCGCAAATGAAGATCTCC  >  NC_000913/3458150‑3458636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑