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%	40.2 / NA	13	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (7/6);  total (7/6)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATC  >  CP000730/479438‑479676                                                                                                                    |                                                                                                                            aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                    >  2:84056/1‑141 (MQ=255)      aGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATa                                                                                               <  2:93825/141‑1 (MQ=255)                    cAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAgaa                                                                                 <  1:25969/141‑3 (MQ=255)                        tGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgc                                                                             >  2:57336/1‑141 (MQ=255)                                        tAAATGGACGAAACTTTATATCGATCGATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAGTTAGCGCAACATGACCATAGTTTTACTAAAGCGCAGCGCCAAGTGATTAGAgg                                                             <  2:6061/141‑1 (MQ=255)                                         aaaTGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGAAAATGCCGAAGCGTGAGCAAAGTTTTGACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCCAGTGATTAAAGGc                                                            <  2:90014/141‑1 (MQ=255)                                               aCGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTAccc                                                      >  2:13429/1‑141 (MQ=255)                                                cGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCa                                                     >  1:86049/1‑141 (MQ=255)                                                 gAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCaa                                                    <  1:84056/141‑1 (MQ=255)                                                                                   aCAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACt                  <  2:57843/141‑1 (MQ=255)                                                                                      aTGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAt               >  1:16779/1‑141 (MQ=255)                                                                                              gCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAAt       >  2:50741/1‑141 (MQ=255)                                                                                                   aGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATc  >  2:98382/1‑141 (MQ=255)                                                                                                                    |                                                                                                                            AGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATC  >  CP000730/479438‑479676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑