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%	73.4 / NA	27	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (14/13);  total (14/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855951‑2856220                                                                                                                                         |                                                                                                                                      agaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGTGCCaaaa                                                                                                                                    <  2:231690/140‑1 (MQ=255)     gCATGGCGTTGGTCCTAAAGCTATATCAATATTGGACCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTc                                                                                                                                <  2:66292/140‑1 (MQ=255)         ggCGTTAATCCTAAAGCTATATCAATGTAGGAACAAGCTTTATTTCATCACCAACTACATTTTAAAACGGAAGTTCAGTCATCGTTACCTTTTAAGTTAAAAGGCGATGTCTCATGCCATCATGCGCCAAAAAGtacaca                                                                                                                            >  2:122595/1‑135 (MQ=255)                     aatgCTATATCAATAGTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAGGCATGCGCCAAAACGTCAACAAATGATAGGttt                                                                                                                <  2:292374/137‑1 (MQ=255)                              tCAATATTGGAAAAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                       <  2:75236/140‑1 (MQ=255)                                aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACTGAAGTTCAGTCATCATTACCTTTTAAGTGAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  2:16125/140‑1 (MQ=255)                                aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  1:188958/140‑1 (MQ=255)                                aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  1:34551/140‑1 (MQ=255)                                     tGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagca                                                                                                >  2:162901/1‑140 (MQ=255)                                               tttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGata                                                                                      >  1:128871/1‑140 (MQ=255)                                                  aTTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg                                                                                   >  1:272805/1‑140 (MQ=255)                                                           ccAACTACTTTTTAAATCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTAc                                                                          <  1:56586/140‑1 (MQ=255)                                                                   aTTTTAAAACGGAAGTTCAGTCATCATTACCTCTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                  <  2:22693/140‑1 (MQ=255)                                                                       tAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGTGGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTGCCTGGTTa                                                              >  2:240702/1‑140 (MQ=255)                                                                         aaaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGAGGTGTCATGCAATCATGCTCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTaca                                                            >  2:76437/1‑140 (MQ=255)                                                                            cGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAGTATTACGTTCATTGGtagaaaca                                                         >  2:191451/1‑133 (MQ=255)                                                                                          tcatTACCTGTTCAGTGAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc                                           <  1:302862/140‑1 (MQ=255)                                                                                             ttACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGt                                        >  1:291887/1‑140 (MQ=255)                                                                                                         ttAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCtt                            >  1:72094/1‑140 (MQ=255)                                                                                                           aaCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCTCTTTg                          >  1:291010/1‑140 (MQ=255)                                                                                                                gagaTGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACata                     <  2:183318/140‑1 (MQ=255)                                                                                                                    tgtgTCATGCAATCAAGCGCCAACACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGACATTGAATTCTTACGTTTACTGGTTACAACAGAATTAATTAGGTCTGTCCCTGGCCGCTTTGAAATATACg                 >  2:65919/1‑140 (MQ=255)                                                                                                                      tgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGa               >  1:31543/1‑140 (MQ=255)                                                                                                                                tCATGCGCCAAAACGTTAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat     <  1:126102/140‑1 (MQ=255)                                                                                                                                 cATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAAtttt    >  1:142737/1‑140 (MQ=255)                                                                                                                                  aTGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTa   <  1:75023/140‑1 (MQ=255)                                                                                                                                   tGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGCATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  >  1:90421/1‑140 (MQ=255)                                                                                                                                   tGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  <  1:145276/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                      AGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855951‑2856220

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: ‑