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%	103.0 / NA	34	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/20);  total (14/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAC  >  CP000730/479422‑479687                                                                                                                                    |                                                                                                                                        cAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGc                                                                                                                                <  1:278702/141‑1 (MQ=255)     aataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAttt                                                                                                                            >  2:205998/1‑141 (MQ=255)      ataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTa                                                                                                                           >  2:102365/1‑141 (MQ=255)      ataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATAGTTGCATTTa                                                                                                                           >  2:188608/1‑141 (MQ=255)       taGATGAACAAGGTGAGCCACTTAGCAAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAg                                                                                                                          >  2:238125/1‑141 (MQ=255)             aaCAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGAAAGAGACAAGTTTTTACCATACATGGTTGCATTTAggcgaac                                                                                                                    >  1:104418/1‑135 (MQ=255)                 aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                                <  1:174225/141‑1 (MQ=255)                 aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                                <  1:194436/141‑1 (MQ=255)                   gTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGAcc                                                                                                              <  1:40782/141‑1 (MQ=255)                        ccACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGt                                                                                                         <  1:222115/141‑1 (MQ=255)                                            tCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATATATGGTTGCATTTAGCGCAACATGACTTTTGTTTTACTAAAGCACAGCGCCa                                                                                     <  2:271448/141‑1 (MQ=255)                                              gTCATAGGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTCACTAAAGCACAGCGCCAAg                                                                                   <  1:203318/141‑1 (MQ=255)                                              gTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                   <  1:184601/141‑1 (MQ=255)                                                    agATCAAATCGACCAAACCTTATATCGATCAATTTCTATCGAGTTCAACAATGCCGAAGCGTCCGCAAACTTTTTACCCAACATCGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTa                                                                             <  2:366662/140‑1 (MQ=255)                                                         aaaTGGACGAAACTTTCTATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGc                                                                        <  1:115871/141‑1 (MQ=255)                                                            tGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTa                                                                     >  2:217107/1‑141 (MQ=255)                                                                cGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACAGGACCATAGTTTTACTACAGAACAGCGCCAAGTCAGAAAAGGCGTCCCCa                                                                 >  1:50577/1‑141 (MQ=255)                                                                      tttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACTGCGCCAAGTGATTAAAGGCTTACCCAATGATc                                                           <  1:273999/141‑1 (MQ=255)                                                                          tatCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGa                                                       >  1:291031/1‑141 (MQ=255)                                                                                      tatATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATaga                                           <  2:188360/139‑1 (MQ=255)                                                                                        tATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGt                                         >  2:141378/1‑141 (MQ=255)                                                                                                  gACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAAc                               <  2:181350/141‑1 (MQ=255)                                                                                                       tGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tt                         <  1:217030/141‑1 (MQ=255)                                                                                                        gCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGATTTACGAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAACGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑ttt                        >  2:215554/1‑141 (MQ=255)                                                                                                         ccGAAGCGTGAGCAAAGTTTTTACCGTACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTGACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  2:244463/141‑1 (MQ=255)                                                                                                         ccGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  1:195139/141‑1 (MQ=255)                                                                                                         ccGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  2:189739/141‑1 (MQ=255)                                                                                                          cGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACACAATGATCCTGAAGTGACGATAGGGTCAGTATTAACTCC‑ttttt                      >  1:174975/1‑141 (MQ=255)                                                                                                           gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGTGTCAGTCTTAACTCA‑TTTTTc                     >  1:18684/1‑141 (MQ=255)                                                                                                                 tGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCCGGATACACTCA‑TTTTTCAATAGa               >  2:1689/1‑141 (MQ=255)                                                                                                                       aaGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGACATGACGATAGAGTCAGTATTAACTCATTTTTTCAATAGATCAgg          <  1:216377/141‑1 (MQ=255)                                                                                                                           ttttACCACACATGGTTGCATTTAGCGCAACATGACCATAGTTTTAATAAAGCGCAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGAc     <  1:165963/141‑1 (MQ=255)                                                                                                                             ttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTa   >  2:189657/1‑141 (MQ=255)                                                                                                                              tACCATACCTGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAc  <  1:313173/141‑1 (MQ=255)                                                                                                                                    |                                                                                                                                        CAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAC  >  CP000730/479422‑479687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑