Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,454,722	T→C	Y226C (TAC→TGC)	gspA ←	Type II secretion system protein GspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,454,722	0	T	C	100.0%	92.1 / NA	27	Y226C (TAC→TGC)	gspA	Type II secretion system protein GspA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/11);  total (16/11)

GGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGT  >  NC_000913/3454477‑3454961                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                ggACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATc                                                                                                                                                                                                                                            >  2:116914/1‑251 (MQ=255)    ccTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCAtt                                                                                                                                                                                                                                         >  1:224271/1‑251 (MQ=255)         tACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGcc                                                                                                                                                                                                                                     >  2:344650/1‑250 (MQ=255)                       gTATAACACGCTTAGCGCCTCACTATCGCGCATCACCAAATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCtgtg                                                                                                                                                                                                                       >  1:323489/1‑250 (MQ=255)                             cacGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGc                                                                                                                                                                                                                >  1:358758/1‑251 (MQ=255)                                        ccTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCg                                                                                                                                                                                                     <  1:99149/251‑1 (MQ=255)                                           aaCTATCGCGCATCACCACATGAGCAATCTCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCCGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAAACATTCGCCATTGTTTTGCCGTGAAAACGCTGTTCTGCTCGGCt                                                                                                                                                                                                  >  2:220682/2‑251 (MQ=255)                                            ccTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCtt                                                                                                                                                                                                 <  1:408204/250‑1 (MQ=255)                                                    gcATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGtaat                                                                                                                                                                                         <  1:135801/251‑1 (MQ=255)                                                          ccacATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGGTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCg                                                                                                                                                                                    >  1:401692/1‑250 (MQ=255)                                                            acaTGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAAt                                                                                                                                                                                 >  1:264072/1‑251 (MQ=255)                                                             caTGAGCAATATCCTTAGTCATATCTTGTGTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCAAAtt                                                                                                                                                                                <  2:212950/251‑1 (MQ=255)                                                                       atCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCtgtg                                                                                                                                                                                                                       >  2:265974/1‑202 (MQ=255)                                                                       atCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCtgtg                                                                                                                                                                                                                       <  1:265974/202‑1 (MQ=255)                                                                         ccTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCa                                                                                                                                                                    <  1:240012/251‑1 (MQ=255)                                                                          cTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCa                                                                                                                                                                    >  2:135494/1‑250 (MQ=255)                                                                                                                     cACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCg                                                                                                                        <  2:224271/251‑1 (MQ=255)                                                                                                                           ggAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCACGCGCCAGCTTTCTGCGTTCGCCCCGACATAATAAAGCTATCCGttta                                                                                                                    >  2:71442/1‑248 (MQ=255)                                                                                                                                          gCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTaa                                                                                                   <  1:116914/251‑1 (MQ=255)                                                                                                                                                                  cAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATAtt                                                                           <  1:35775/251‑1 (MQ=255)                                                                                                                                                                        caGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGAcc                                                                     >  1:288677/1‑251 (MQ=255)                                                                                                                                                                                                              aaGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGAc                               >  1:53782/1‑251 (MQ=255)                                                                                                                                                                                                                     aTTTTCCGGGGGCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGCCAGACGTTCTAt                        >  1:164685/1‑251 (MQ=255)                                                                                                                                                                                                                                gCGGTTATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGtt             <  1:135494/251‑1 (MQ=255)                                                                                                                                                                                                                                     tATCACCCAATATGCGGCAAATCATTCGCCATTGTTTTGCTGCGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCCTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATg        >  1:277545/1‑251 (MQ=255)                                                                                                                                                                                                                                          cccAATATGCGGCAAATAAATCGCCATTGTTTTGCTGTAAAAACGCTGGTCTGCTCGGCTTGCTGTAATACGCGATGTGTTTCGCCCGCAAGCGCCAGCTTTCTGCGATCGTCCTGAAAGAAAAAAGCTATCCGTTTCAGGACTCTGGCGGTTAAAAGGAGATCGGCTTGGGCAATAGTCTGACCTTCAGGGATGCTTGCCTTCAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGGTCTATGCCCTg   <  2:151895/251‑1 (MQ=255)                                                                                                                                                                                                                                           ccAATATGCGGCAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGGGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCNTGt  >  2:378906/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                GGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCACATGAGCAATATCCTTAGTCATATCTTGTTTAACTACTGGCGTTACGGGTATCAGCCACGCAGGAACGGGTAACGTAGCTGTAAAAGAGGACAGCAGTAGCCAACCACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGT  >  NC_000913/3454477‑3454961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑