Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,456,451	C→T	N25N (AAC→AAT)	gspD →	Type II secretion system protein GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,456,451	0	C	T	100.0%	63.2 / NA	19	N25N (AAC→AAT)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/7);  total (12/7)

ATATCGCCCTCAGGATCAATAATCTTTCGCTGACCCACCCTGATGAGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAACGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGC  >  NC_000913/3456206‑3456687                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                             atagcGCCCTCAGGATCAATAATCTTTCGCTGACCCACCCTGATGAGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCGTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACa                                                                                                                                                                                                                                         <  1:139746/247‑1 (MQ=255)              gATCAATAATCTTTCGCTGACCCACCCTGATGAGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAAc                                                                                                                                                                                                                            >  2:174094/1‑251 (MQ=255)                            cGCTGACCCACCCTGATGAGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCg                                                                                                                                                                                                               <  2:137568/250‑1 (MQ=255)                                             gaGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACACTCCGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTgg                                                                                                                                                                                             >  2:43111/1‑251 (MQ=255)                                                     acaGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTg                                                                                                                                                                                     >  2:25572/1‑251 (MQ=255)                                                        ggCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGt                                                                                                                                                                                  >  1:17208/1‑251 (MQ=255)                                                                       gCTAACTCAACAAAGTGCGCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCaa                                                                                                                                                                    <  1:207703/250‑1 (MQ=255)                                                                                                  aaTTCGTCGCAAAGGCGCACCCCGCTTGATAAATGTTTCCGTCGGGGACCTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCACTAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTAc                                                                                                                                          >  2:13414/1‑249 (MQ=255)                                                                                                      cgtcgCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAAATTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGa                                                                                                                                     >  1:112945/1‑250 (MQ=255)                                                                                                                                aaaTGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCACGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATAc                                                                                                           <  1:174094/250‑1 (MQ=255)                                                                                                                                        ccGTCGGGGAACTGACAGGAATGAAGGGACTACATCATTAAAAGATTCAATAAAATCACCTGCTGCTTGCTGGCATACCTACTCATGCCTTGTTCAGGACACGCTTAGAATGAAAAATACGGCACGAACTTCAATAACTCCTATATCCGCCAGTTCGTGGAAATAGTTGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGTTACAGGGAACCATTTCCGTACGCTGGAATGAAACGTTTAGccc                                                                                                  <  2:129124/251‑2 (MQ=255)                                                                                                                                                      aCAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGtactac                                                                                     <  1:210710/250‑1 (MQ=255)                                                                                                                                                        aGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTAcc                                                                                    >  1:235961/1‑249 (MQ=255)                                                                                                                                                         ggAATGAATGGCCTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGt                                                                                 >  2:249237/1‑251 (MQ=255)                                                                                                                                                                  ggACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGGACGCAGTAATGATACGTTTATCCAACAGGAGTACTACCAGTTCTTTTTa                                                                         >  2:30544/1‑250 (MQ=255)                                                                                                                                                                      tGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTCCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTAt                                                                    >  2:173148/1‑251 (MQ=255)                                                                                                                                                                                                                   gcaCTACTCATGCCTTGTGCAGGACACGCTGAGAATGAACAATACGGCGAGCACTTCAATAACGCCGATATACGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGAACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACAAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGttt                       >  1:33616/1‑251 (MQ=255)                                                                                                                                                                                                                               ccTTGTGTAGGACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACTGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGt           >  2:170369/1‑251 (MQ=255)                                                                                                                                                                                                                                        ggACACGCTGAGAATGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGc  <  1:181777/251‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                             ATATCGCCCTCAGGATCAATAATCTTTCGCTGACCCACCCTGATGAGGTTTCACAGGCATTAAGTTTACTGCTAACTCAACAAAGTGCTCAGTTTACAATTCGTCGCAACGGCGTACCCCGCTTGATAAATGTTTCCGTCGGGGAACTTACAGGAATGAATGGACTGCGTCATGAAAGGACTCAATAAAATCACCTGCTGCTTGCTGGCAGCACTACTCATGCCTTGTGCAGGACACGCTGAGAACGAACAATACGGCGCGAACTTCAATAACGCCGATATCCGCCAGTTCGTGGAAATAGTGGGTCAGCATCTTGGCAAAACGATCCTGATCGACCCTTCGGTACAGGGAACCATTTCCGTACGCAGTAATGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGC  >  NC_000913/3456206‑3456687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑