Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	479,553	G→A	100%	A194T (GCA→ACA)	USA300HOU_RS02280 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	479,553	0	G	A	100.0%	87.8 / NA	29	A194T (GCA→ACA)	USA300HOU_RS02280	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/16);  total (13/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTAC  >  USA300TCH1516_ALE/479418‑479687                                                                                                                                        |                                                                                                                                       gATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATgg                                                                                                                                   <  2:180902/141‑1 (MQ=255)    gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTg                                                                                                                                <  1:16412/141‑1 (MQ=255)            aGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                        <  1:51257/141‑1 (MQ=255)            aGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                        <  1:200316/141‑1 (MQ=255)            aGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAAGCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgc                                                                                                                        <  1:47783/141‑1 (MQ=255)              aTGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATTAGTACAAGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                      <  2:127229/141‑1 (MQ=255)               tGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACGATGCCGAAGCGTGTGCGAAGTTTTTACCATACATGGTTGCATTTAGCGCa                                                                                                                     >  2:84044/1‑141 (MQ=255)                         gAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTGTATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCAt                                                                                                           <  1:270133/141‑1 (MQ=255)                           gCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTATCGCAACATGACCATAg                                                                                                         >  2:163387/1‑141 (MQ=255)                                ttAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTa                                                                                                    >  2:251906/1‑141 (MQ=255)                                 tAGCGAACAAGTGAAGCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTAc                                                                                                   <  1:130427/141‑1 (MQ=255)                                                 cGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCaa                                                                                   <  1:103001/141‑1 (MQ=255)                                                  gTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                  <  1:179671/141‑1 (MQ=255)                                                            tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                        >  2:207077/1‑141 (MQ=255)                                                                  gACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGAGCCAAGTGATTAAAGGCTTAcc                                                                  >  1:92254/1‑141 (MQ=255)                                                                            tataTCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACAATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAGTGATCCt                                                        >  2:58477/1‑141 (MQ=255)                                                                              tatCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGa                                                      >  1:8777/1‑141 (MQ=255)                                                                               atCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCCACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGaa                                                     <  1:263280/141‑1 (MQ=255)                                                                                         ttCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATag                                           <  1:157132/141‑1 (MQ=255)                                                                                         tcccaTCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACCTGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATag                                           <  1:18751/137‑1 (MQ=255)                                                                                                  gTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTAt                                  <  2:92142/141‑1 (MQ=255)                                                                                                     ggACAATGCCGAAGCGTGCGAATAGTACATACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATCGAGGCAGTCTTaa                               >  1:135820/1‑141 (MQ=255)                                                                                                               gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTGACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATCACGATAGAGTCAGAATTAACTCAttttta                     >  2:27256/1‑140 (MQ=255)                                                                                                                  gCGTGAGCAAAGTTTTTACCACACATGGTTCCATATAGAGCAACAGCACCATCGTTCTACTAAAGCCCAGCGCCAAGTCATAGAACACTCACCCCATGATCCTGAAATGCCACTACAGTCAGAATCACCTCAtttttaaca                  >  2:184751/1‑137 (MQ=255)                                                                                                                       aGCAAAGTTTTTACAATACATGGTTGCATCTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATc             >  1:149808/1‑141 (MQ=255)                                                                                                                              tttttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGa      >  2:253088/1‑141 (MQ=255)                                                                                                                                 ttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAATTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTa   <  1:214054/141‑1 (MQ=255)                                                                                                                                  tACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTAc  >  1:27533/1‑141 (MQ=255)                                                                                                                                  tACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTAc  <  1:251906/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       GATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTAC  >  USA300TCH1516_ALE/479418‑479687

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: ‑