Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,856,087	T→A	100%	P80P (CCT→CCA)	rpoA_2 →	DNA‑directed RNA polymerase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,856,087	0	T	A	100.0%	94.6 / NA	29	P80P (CCT→CCA)	rpoA_2	DNA‑directed RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (15/14);  total (15/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTA  >  USA300TCH1516_ALE/2855952‑2856219                                                                                                                                        |                                                                                                                                     gaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACg                                                                                                                                 >  1:202255/1‑141 (MQ=255)       tGGCGTTGGTCCTAAAGCTATATCAATATGGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTACCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaaca                                                                                                                           <  2:259529/141‑1 (MQ=255)        ggCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGCTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaacaa                                                                                                                          >  2:145403/1‑141 (MQ=255)            ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                      <  1:172193/141‑1 (MQ=255)            ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                      <  1:275192/141‑1 (MQ=255)                        cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGTGATGTGTCATGCAATCATGCGCCAAAACGTCCACAAATGATAGATTTTATAg                                                                                                          <  1:173490/141‑1 (MQ=255)                            atCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                      >  2:13264/1‑141 (MQ=255)                                atatTGGAACAAGCTTTATTTCAGCACCAACTACATCTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAca                                                                                                  <  2:14794/141‑1 (MQ=255)                                        aCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAtt                                                                                          >  2:93995/1‑141 (MQ=255)                                         cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAAACATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTa                                                                                         <  1:183838/141‑1 (MQ=255)                                         cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAAACATGCGCCAAAACGTCAACAAATGAGAGATTTTATAGTTGTTACAGCAGCATTa                                                                                         <  1:183837/141‑1 (MQ=255)                                           tgcgttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCCTGCAATCATGCGCCAAAACGTCAACACATGATAGCTTTTATAGTTGTTACATCAGCATTAGa                                                                                       >  2:260801/5‑141 (MQ=255)                                           aGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGa                                                                                       >  2:40499/1‑141 (MQ=255)                                                       gCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattatt                                                                           >  1:139918/1‑141 (MQ=255)                                                        cACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAttatta                                                                          <  1:13264/141‑1 (MQ=255)                                                        cACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAttatta                                                                          >  2:168398/1‑141 (MQ=255)                                                               tACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCAc                                                                   <  1:133166/141‑1 (MQ=255)                                                                        aaaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAAGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTacaa                                                          >  1:268166/1‑141 (MQ=255)                                                                         aaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTGGTTAAAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTccaac                                                         >  1:40911/1‑141 (MQ=255)                                                                           cGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAg                                                       <  1:164978/141‑1 (MQ=255)                                                                             gAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGaa                                                     >  1:260538/1‑141 (MQ=255)                                                                                          catTACCTTTTAAGTTAACGAGAGATGTGTCATGCAATCATGCGCCAAAACGTCGACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTg                                        >  1:184573/1‑141 (MQ=255)                                                                                              aCCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATAAGAGATTGTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGGTCACTGGTTACAACAGAATTTATTTGGTCTGTccc                                    >  1:66023/1‑141 (MQ=255)                                                                                                 ttttAAGTTAACAGGAGATGTGGCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTgg                                 <  2:240009/141‑1 (MQ=255)                                                                                                    tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg                              <  1:93995/141‑1 (MQ=255)                                                                                                           aCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGAc                       >  2:76698/1‑141 (MQ=255)                                                                                                                             aaTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCCGCGTTTGATATTGAATTATTACTTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAata     <  1:266344/141‑1 (MQ=255)                                                                                                                              aTCATGCGCCAAAACGTCAACAAACGATAGATTTTAAAGTTGTTACAGCAGCATTAGATATTGCATCACTAGCTGCACGGGTTTACACATAGTTTTTTTTGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat    <  1:280312/141‑1 (MQ=255)                                                                                                                                cATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTa  >  1:213141/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                     GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTA  >  USA300TCH1516_ALE/2855952‑2856219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑