Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	479,553	G→A	100%	A194T (GCA→ACA)	USA300HOU_0458 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	479,553	0	G	A	100.0%	74.8 / NA	26	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/13);  total (13/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479419‑479686                                                                                                                                       |                                                                                                                                      aTGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATgg                                                                                                                                  >  2:125644/1‑140 (MQ=255)   gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGtt                                                                                                                                <  1:194552/140‑1 (MQ=255)     aataatAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGc                                                                                                                              <  1:27330/140‑1 (MQ=255)         ataGATGAACAAGGTGAGCCACTTAGCGAAAAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAttt                                                                                                                          <  1:87932/140‑1 (MQ=255)            gATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                       >  1:140219/1‑140 (MQ=255)              tGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                     <  2:28147/140‑1 (MQ=255)               gAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCa                                                                                                                    <  2:164606/140‑1 (MQ=255)                 aCAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCAGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAAc                                                                                                                  >  1:225021/1‑140 (MQ=255)                           ccACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAGTGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAg                                                                                                        >  2:93574/1‑140 (MQ=255)                           ccACTTAGCGAACAAGAGAATCGTCAAATGATTAAATGGACGAAACTTAATATCGATGAATTTCTATCGAGTTGGACAATGCCGACGAATGAGCACATGTTGTAGCATACATGGTTGCATTTACAGCCACATGACAATAg                                                                                                        >  2:60625/1‑140 (MQ=255)                                            gAATCGTCAAATGATTAAATGGACGAAACTTTATATATATCAAATTCTACAGTGTTATACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATTACCATAGTTTTACTTAATCACAgc                                                                                       >  1:68640/1‑140 (MQ=255)                                              aacctCATATGACTAAATCGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgcgc                                                                                     <  2:240060/136‑1 (MQ=255)                                                  tCAAATGATTAAATGGACGAAACTTTATAACGATCGATTGCTATCGAGGTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                 <  1:49307/140‑1 (MQ=255)                                                     aaTGATTAAATGAACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGGTGTACTCAAGCACAGCGCCAAGTGa                                                                              >  2:23622/1‑140 (MQ=255)                                                           tAAATGGACGAAACTTTATATCGATCAATTTCTAGCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAg                                                                        <  1:118757/140‑1 (MQ=255)                                                            aaaCGGGCGAAGCTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGGTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  1:77132/140‑1 (MQ=255)                                                                          ttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATc                                                         >  2:58245/1‑140 (MQ=255)                                                                              atCGATCAATTTATATAGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTAATATACATGGTTGCATTTAGCGCAACATGACCGTCGTTTTACTAAAACCCAGGGCCAAGTGATTAAAAGCTTcccctcggctactac                                                     >  2:45300/1‑129 (MQ=255)                                                                                 gATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGATCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAAt                                                  <  1:87204/140‑1 (MQ=255)                                                                                           tATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATagag                                        >  1:281340/1‑140 (MQ=255)                                                                                             tCGAGTTGGACAATGCGGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAATATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTc                                      <  2:225051/140‑1 (MQ=255)                                                                                                             cGAAGCGTGAGCAAAGTTTGTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAtttt                      <  2:209065/140‑1 (MQ=255)                                                                                                              gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAttttt                     >  2:115071/1‑140 (MQ=255)                                                                                                                       gCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAGTGACGATTGAGTTAGTATTAACTCATTTTTCTAtgggtg            >  1:133318/1‑135 (MQ=255)                                                                                                                              ttttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGAGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTAAATAGATCAGGACGa     >  2:260027/1‑140 (MQ=255)                                                                                                                                 tACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTa  <  1:13639/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                      ATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479419‑479686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑