Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,004,304	G→A	A145T (GCG→ACG)	fliD →	flagellar filament capping protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,004,304	0	G	A	100.0%	106.8 / NA	30	A145T (GCG→ACG)	fliD	flagellar filament capping protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/19);  total (11/19)

GCGATCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCGCGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGCATCATT  >  NC_000913/2004229‑2004378                                                                            |                                                                           gCGATCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCt                                                                       <  2:317117/81‑1 (MQ=255)   gATCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTaa                                                                     >  1:317164/1‑81 (MQ=255)     tCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACt                                                                   <  1:317119/81‑1 (MQ=255)     tCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACt                                                                   <  1:317118/81‑1 (MQ=255)       gCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCa                                                                 >  2:317165/1‑81 (MQ=255)        ccaccaGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCAt                                                                <  2:317120/81‑1 (MQ=255)            caGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGtt                                                            <  2:317121/81‑1 (MQ=255)             aGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTa                                                           <  2:317122/81‑1 (MQ=255)              gCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTaa                                                          <  1:317123/81‑1 (MQ=255)                gACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGc                                                        >  2:317158/1‑81 (MQ=255)                   aGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCggg                                                     <  1:317124/81‑1 (MQ=255)                     tAACCTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGAt                                                   <  2:317125/81‑1 (MQ=255)                      aaaCTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATc                                                  >  1:317152/1‑81 (MQ=255)                              cATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGc                                          >  1:317156/1‑81 (MQ=255)                               aTTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGcc                                         <  2:317126/81‑1 (MQ=255)                               aTTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGc                                          >  2:317160/1‑80 (MQ=255)                                    acaaGGCGGCGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATcaa                                    <  2:317127/81‑1 (MQ=255)                                        ggcggcGACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCaataac                                >  1:317167/1‑81 (MQ=255)                                             cgACAAAGATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCaa                            >  2:317162/1‑80 (MQ=255)                                                    gATCCGATTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGc                    >  1:317174/1‑81 (MQ=255)                                                          aTTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAgc              <  2:317128/81‑1 (MQ=255)                                                          aTTACCATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAgc              >  1:317169/1‑81 (MQ=255)                                                              ccATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCaa          <  1:317130/81‑1 (MQ=255)                                                              ccATTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCa           <  2:317129/80‑1 (MQ=255)                                                                aTTGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGc        <  1:317131/81‑1 (MQ=255)                                                                  tGATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGcat      >  2:317166/1‑81 (MQ=255)                                                                   gATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGcat      <  1:317133/80‑1 (MQ=255)                                                                   gATATCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGcat      <  1:317132/80‑1 (MQ=255)                                                                    atatCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGcatca    <  2:317134/81‑1 (MQ=255)                                                                       tCAGCACGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGCATCAtt  <  1:317135/80‑1 (MQ=255)                                                                            |                                                                           GCGATCGCCACCAGCGACAGTAAACTCACCATTCAACAAGGCGGCGACAAAGATCCGATTACCATTGATATCAGCGCGGCTAACTCATCGTTAAGCGGGATCCGTGATGCCATCAACAACGCAAAAGCAGGCGTAAGCGCAAGCATCATT  >  NC_000913/2004229‑2004378

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑