Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,465,279	T→C	G66G (GGT→GGC)	gspM →	Type II secretion system protein GspM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,465,279	0	T	C	100.0%	68.3 / NA	24	G66G (GGT→GGC)	gspM	Type II secretion system protein GspM
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/13);  total (11/13)

AAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATT  >  NC_000913/3465037‑3465520                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  aaaaGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCgg                                                                                                                                                                                                                                           <  1:69128/251‑1 (MQ=255)        ccGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCt                                                                                                                                                                                                                                    <  1:207544/251‑1 (MQ=255)                        ggACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGccc                                                                                                                                                                                                                     <  1:375824/250‑1 (MQ=255)                                       cAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCtt                                                                                                                                                                                                      <  1:289901/250‑1 (MQ=255)                                        agagAAATGATTAAATCATGGTGGTCAGAAAAATCCACATCGGTAAAACAGATCGGTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTATTGGCATGGGGTGAGAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGTTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTtca                                                                                                                                                                                                    <  2:90360/248‑2 (MQ=255)                                          ggAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCg                                                                                                                                                                                                  <  1:55055/251‑1 (MQ=255)                                                                     aaaaTCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTTTCCCCCGGCGTTTTTTTTTGGGTTGGGGGGGTAAAACCGATAAATACCTACCTTGTAGAGTATCAGTCCCCCCCGCCAAAAATTAAAAAGGACATCAAATTGATGCAGGATCAAGCGAGCACCCATGGCTTAATCGGGCATCCTGCGCTTACGCAACCCCACAAAAACATCCTTCCCGGGGTAGCAAAAAGTGAGAAATTgggtg                                                                                                                                                                       >  2:137498/1‑248 (MQ=255)                                                                          ccACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCCGGGGTTTTTGTTTGCTTGGGGGGGTAACACCCATAGATAACTACATTTTAGAGGATCTGTTCCCCCCGCAAAAAAATAAGAAAGACATCAAATTGATGCAGGGTCAAGCGAGAACCCATGGCTTTCTCCGTCATCCTTCCCTTACGCAGCCCCTCAAAAATATCCTTCTCGCGGAAGCCAAACGTGAGAATTTTGCttttacc                                                                                                                                                                  >  1:365690/1‑245 (MQ=255)                                                                                cGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAAc                                                                                                                                                                                      <  1:340663/225‑1 (MQ=255)                                                                                cGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGATTGGCGTTTTTTTTTGGCTTGGGGGGGTAAAAACGATTGATACCTACATTTCAGAGCATCAGTCCCACCCGCAAAAAATTAAAAAGGACATCAAATGGATGCAGGATCAAGAGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGa                                                                                                                                                             >  1:41388/1‑250 (MQ=255)                                                                                           aTCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGGTTTTTTTTGGGTTGGGGGGGTAAAACCGATAGATACCTACATTTTAGAGCCTCACTCCCACGCGCCAAAAAATAATAAGGACATACAATGGATTCAGGATCAAGCGAGCACCCCCGGCTTACTCGGCCATTCTTCGCTTACGCCGCCCACCACAAAAATCCTTTTCGCGGAAACAAAAAGCGAGAATTTGGCTATCCCACTGGAAAACGGCCCgg                                                                                                                                                  >  2:28173/1‑250 (MQ=255)                                                                                                                                tttGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGTACAATACTCTGACAATTCATCCTGTCACAGCTCCCCt                                                                                                             <  2:367518/250‑1 (MQ=255)                                                                                                                                     tgGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGaaa                                                                                                        >  2:363474/1‑250 (MQ=255)                                                                                                                                       gCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACg                                                                                                     >  2:90427/1‑251 (MQ=255)                                                                                                                                            gggTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTcc                                                                                                <  2:137746/251‑1 (MQ=255)                                                                                                                                                                    aCATTGCCGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCCCCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATAACGCTGGCAAACGGCCCGGTCAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTa                                                                        <  2:331061/251‑1 (MQ=255)                                                                                                                                                                                      cccACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTAtt                                                      <  1:363474/251‑1 (MQ=255)                                                                                                                                                                                       ccACGCGCAAAAAATTAAGAAGGTCATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTg                                                     <  2:6407/251‑1 (MQ=255)                                                                                                                                                                                                   aaTTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGt                                         >  2:12994/1‑251 (MQ=255)                                                                                                                                                                                                                aTCAAATGGATGCAGGATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCgg                            >  2:150442/1‑251 (MQ=255)                                                                                                                                                                                                                     aTGGAGGCAGGATCAAGCGAGCACGCATGGCTTACTCGGTCATCCTTCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGTCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAGCGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGACGGAAACg                       <  2:4261/251‑1 (MQ=255)                                                                                                                                                                                                                              ggATCAAGCGAGCACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATc               >  2:214149/1‑250 (MQ=255)                                                                                                                                                                                                                               gATCAAGCGAGAACCCATGGCTTACTAGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTAGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCAGACACTTCATCCTGACACAGCTCCCCTCGAAAAGGACTACCGATGGATCACTAAGGCACAGGTAACATAAGGTATTGTTATTGAAGACCTTCAGTTTACTATTGCCGGAAACGAAGAGAtaac             >  2:233859/1‑248 (MQ=255)                                                                                                                                                                                                                                          cACCCATGGCTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCAtt  >  1:67221/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  AAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCGTTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATTGCAGAGCATCAGTCCCACGCGCAAAAAATTAAGAAGGACATCAAATGGATGCAGGATCAAGCGAGCACCCATGGTTTACTCGGTCATCCTGCGCTTACGCAGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATT  >  NC_000913/3465037‑3465520

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑