Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,679,708	G→A	W64* (TGG→TGA)	ssaA2_4 →	Staphylococcal secretory antigen ssaA2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,679,708	0	G	A	100.0%	85.5 / NA	24	W64* (TGG→TGA)	ssaA2_4	Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/15);  total (9/15)

TTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTA  >  USA300TCH1516_ALE/2679568‑2679850                                                                                                                                             |                                                                                                                                               ttCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATg                                                                                                                                         <  1:212358/148‑1 (MQ=255) ttCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATg                                                                                                                                         <  2:171196/148‑1 (MQ=255) ttCTCAGCAGATTCCTGCTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATg                                                                                                                                         <  1:213609/148‑1 (MQ=255)      agcagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTaaa                                                                                                                                    <  1:254269/148‑1 (MQ=255)          aaTTTCACTCATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAAtt                                                                                                                                <  2:14077/147‑1 (MQ=255)                      cAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATg                                                                                                                    <  2:293691/148‑1 (MQ=255)                                       gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAatat                                                                                                   <  2:355144/148‑1 (MQ=255)                                       gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAatat                                                                                                   <  2:201230/148‑1 (MQ=255)                                       gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAatat                                                                                                   <  2:153643/148‑1 (MQ=255)                                          tCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCg                                                                                                <  2:156576/148‑1 (MQ=255)                                                       gCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTacac                                                                                   >  1:286634/1‑148 (MQ=255)                                                               ttatgaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAGCCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAGGaaaa                                                                           <  2:6724/148‑1 (MQ=255)                                                                         aaaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCa                                                                 >  1:370268/1‑148 (MQ=255)                                                                         aaaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCa                                                                 >  1:302216/1‑148 (MQ=255)                                                                                      cATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGc                                                    >  2:62011/1‑148 (MQ=255)                                                                                          gtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGa                                                <  2:206599/148‑1 (MQ=255)                                                                                                         tCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc                                 >  2:258013/1‑148 (MQ=255)                                                                                                                  aGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgttgtt                        <  2:115759/148‑1 (MQ=255)                                                                                                                   gTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                       <  2:42024/148‑1 (MQ=255)                                                                                                                     cGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATATCGCAGTTGTTGaa                     >  1:20927/1‑148 (MQ=255)                                                                                                                         aaaCCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAg                 >  2:16798/1‑148 (MQ=255)                                                                                                                         aaaCCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAg                 >  2:203246/1‑148 (MQ=255)                                                                                                                            ccTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtat              >  1:358863/1‑148 (MQ=255)                                                                                                                                        aGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgta  <  2:52422/148‑1 (MQ=255)                                                                                                                                             |                                                                                                                                               TTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTA  >  USA300TCH1516_ALE/2679568‑2679850

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