Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	127,420	G→T	L411F (TTG→TTT)	lctP_1 →	L‑lactate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	127,420	0	G	T	100.0%	59.6 / NA	22	L411F (TTG→TTT)	lctP_1	L‑lactate permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (8/14);  total (8/14)

AATTACGAAGTTAAAATGGAAAAGTGCAGGTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTGACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTGGTGTGTTTATGACTGGTTCAGTTGTAAATAACAATACTTTATTCGCAC  >  USA300TCH1516_ALE/127294‑127544                                                                                                                               |                                                                                                                             aaTTACGAAGTTAAAATGGAAAAGTGCAGGTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGc                                                                                                                      <  1:210926/135‑1 (MQ=255)      cGAAGTTAAAATGGAAAAGTGCAGGTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTg                                                                                                                 <  1:161606/135‑1 (MQ=255)          gTTAAAATGGAAAAGTGCAGGTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACa                                                                                                             <  2:27673/135‑1 (MQ=255)             aacattgAAAAGTGCAGGTGCTTTATTGGTCTAATCAATTAAAGAATTATGTTTATCGTTTCTTACAATTTCAGCTATTTTATTTTTTGCTATAGTTATTACATATGGTGGTTTTACTGTAGCAATTGGACAAgg                                                                                                          <  1:66527/129‑1 (MQ=255)                     aaaGTGCAGATGCTTTATAGGTCGAAGCAATTAAAGAATTATAGTTACCGAACCTTACAATTTCAGCTATCCTAGCTATTGCTACAGTTATGACATCCGGCGGTTTTACTGTAGCACTTGAACAACATATCGCTa                                                                                                  >  2:9636/1‑135 (MQ=255)                             ggTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTAGCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGa                                                                                          <  2:227053/135‑1 (MQ=255)                                     aTTGATCGGAGTAATTAAAGAATTATGGTTACTGATCCTTACTATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTTGTTGTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAAtttt                                                                                  <  2:153991/135‑1 (MQ=255)                                             aaGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGATATTGCTAAAGCGGGAGCAATTTTCCCattat                                                                          >  1:91524/1‑135 (MQ=255)                                             aaGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGATATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCattat                                                                          >  1:82675/1‑135 (MQ=255)                                                       agtgttATGGTTACCGATGCGTACAATTGCAGCTTTCATAGCTATTGCTAAAGTTATTACATTCGGTGGTTTTACTGTAGCAATTGGACAATGTATTTCTAAAGCGGGAGTAATTTTCCCATTATTCTTTCCAGt                                                                <  2:76344/131‑1 (MQ=255)                                                       aGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTTGTTTTACTGTAGCAATTTGATAATGTATTGTTAAAGCGGGAGCAATTTTCCCAGTATTCTCTCCAGt                                                                <  1:91911/135‑1 (MQ=255)                                                         aaTTATGTTTACCGATCTGTAGAATTTCATCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGTTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTAt                                                              <  2:41067/135‑1 (MQ=255)                                                                 ttACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTgg                                                      <  2:62430/135‑1 (MQ=255)                                                                    ccGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAATTATAACATAAGAAAATATTAATATAACAATTGAACAAGGTATTGCTAAAGAGAGAGGAATTTTCTCATTATTATCTTGAGAATTAGGTTGGAtt                                                   >  1:45935/1‑135 (MQ=255)                                                                     cGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATTACATACGGTGGTTTTACTGTAGCTTTTGGTCAAAGTATTGCTCAAGTTCAAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTg                                                  <  1:101333/135‑1 (MQ=255)                                                                      gATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTgg                                                 >  2:194054/1‑135 (MQ=255)                                                                         ccTTACAATTTCATCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTATCATTTTTTCAGTGTATTGCTAAAGCGGGAGTAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTGgtgt                                              <  1:162782/135‑1 (MQ=255)                                                                                      gCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGTGTAATTTTCCCATTATTCTTTCCAGTATTAGGTTGGATTGGTGTGTTTATGACTGGt                                 <  1:101699/135‑1 (MQ=255)                                                                                                 tATTGCTAAAGTTATGACATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTGGTGTGTTTATGACTGGTTCAGTTGTaaa                      <  1:145991/135‑1 (MQ=255)                                                                                                   ttGCGAAAGTGATGACATACGGGGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAACGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGATGGAATGGTGTGTTTATGACTGGTTCAGTTATAAATa                    >  2:109575/1‑135 (MQ=255)                                                                                                                  cATACGGTGGTTTTACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTGGTGTGTTTATAACTGGTTCAGTTGTAAATAACAATACTGTAttag     >  2:186152/1‑133 (MQ=255)                                                                                                                     aCGGTGGTTTTACTGTAGCAATTGTACAAGGTATTACTAAAGCAGGAACAATTTTCCCATTATTCTCTCCAGTATTAGATTGGAATGGGGTGTTTACCACCGGTTCAGTTGTAAATAACAATACTTTATTCGCAc  >  1:137499/1‑135 (MQ=255)                                                                                                                               |                                                                                                                             AATTACGAAGTTAAAATGGAAAAGTGCAGGTGCTTTATTGGTCGAAGCAATTAAAGAATTATGGTTACCGATCCTTACAATTTCAGCTATCCTAGCTATTGCTAAAGTTATGACATACGGTGGTTTGACTGTAGCAATTGGACAAGGTATTGCTAAAGCGGGAGCAATTTTCCCATTATTCTCTCCAGTATTAGGTTGGATTGGTGTGTTTATGACTGGTTCAGTTGTAAATAACAATACTTTATTCGCAC  >  USA300TCH1516_ALE/127294‑127544

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑