Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,856,087	T→A	100%	P80P (CCT→CCA)	USA300HOU_2698 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,856,087	0	T	A	100.0%	80.9 / NA	27	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (9/18);  total (9/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTCA  >  CP000730/2855970‑2856224                                                                                                                      |                                                                                                                                          tAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAttt                                                                                                                    <  1:189455/141‑1 (MQ=255)   aaGCTATATCAATACTGAAACAAGCTTTATTTCAGAACCAACTACATTTTAAAACGGAAGTTCGGTCATCATTACCTTTTACGTTAACTGGAGAGGAGCAATGCAATCATGCGCCAAAACGTCAACAAAGAGTAGAttttt                                                                                                                  >  2:37807/1‑140 (MQ=255)     gctttgcgaaTACTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTGCCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTtata                                                                                                                <  2:57269/133‑1 (MQ=255)      cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                               <  1:239366/141‑1 (MQ=255)      cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                               >  1:34669/1‑141 (MQ=255)       tataTCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgt                                                                                                              >  2:145373/1‑141 (MQ=255)       tataTCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTAATAgt                                                                                                              >  1:149514/1‑141 (MQ=255)           tCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAACGTTTTCTTTTATAgttgtt                                                                                                          <  2:2444/141‑1 (MQ=255)                   ggAACAAGCTTTATTTCAGCCCCCACTATATTTTACGCCGGAACTCCCGGAAGCATTACCTGGTTAGTTGTCTGGAGATATGGCTTGCAAGCATGGGCCAAGACGGCAACAAATGATAGATTTTATAGTTGTTACagcagc                                                                                                  <  2:93859/141‑1 (MQ=255)                     aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGcatcat                                                                                                >  2:240216/1‑141 (MQ=255)                        aaGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAg                                                                                             <  1:42725/141‑1 (MQ=255)                          gCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGat                                                                                           >  1:76044/1‑141 (MQ=255)                                             tACATTTTAAAACGGACGTTCAGTCATCATTACCGTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCAc                                                                        <  1:9425/141‑1 (MQ=255)                                               cATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                      >  1:197299/1‑141 (MQ=255)                                                 ttttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGt                                                                    <  1:240216/141‑1 (MQ=255)                                                    tAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTac                                                                 <  2:193597/141‑1 (MQ=255)                                                                  attcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATTCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttattt                                                   <  2:115697/139‑1 (MQ=255)                                                                  aGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttattt                                                   <  1:141389/141‑1 (MQ=255)                                                                       tcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTTACTGGTTACAACAGAATTTATTTGGTCt                                              <  1:182884/141‑1 (MQ=255)                                                                           tACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCACCAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTTATTGGTCttgcc                                          >  1:233670/1‑137 (MQ=255)                                                                             ccTTTGAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCt                                        <  2:203953/141‑1 (MQ=255)                                                                                  tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg                                   >  1:75773/1‑141 (MQ=255)                                                                                          cAGTAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACa                           <  1:84497/141‑1 (MQ=255)                                                                                                aTGTGTCATGCACTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTTTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg                     <  1:132187/141‑1 (MQ=255)                                                                                                aTGTGTCATGCAATCATGCACCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg                     <  1:260267/141‑1 (MQ=255)                                                                                                                 gcgcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAAtt    <  2:34669/141‑1 (MQ=255)                                                                                                                   gcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATGCGGACCTCCAATATTAATTCa  <  1:145373/141‑1 (MQ=255)                                                                                                                      |                                                                                                                                          TAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTCA  >  CP000730/2855970‑2856224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑