Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	661,360	T→A	L168M (TTG→ATG)	USA300HOU_RS03170 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	661,360	0	T	A	93.8%	35.0 / ‑6.3	16	L168M (TTG→ATG)	USA300HOU_RS03170	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base A (3/12);  minor base G (1/0);  total (4/12)
Fisher's exact test for biased strand distribution p-value = 2.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAAAGTTACAAATCTATAATGAAAACAAAAATAAAAGCAATAAGATAATCATATTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTATTGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAGTTCATGTATTATTTAAATCAAATGGAATTGAAAAG  >  USA300TCH1516_ALE/661222‑661494                                                                                                                                           |                                                                                                                                       ttaaagttaCAAATCTATAATGAAAACAAAAATAAAAGCAATAAGATAATCATATTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTGATATGTTAGTg                                                                                                                                      >  1:164460/1‑141 (MQ=255)   aaagttaCAAATCTATAATGAAAACAAAAATAAAAGCAATAAGATAATCATATTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGAc                                                                                                                                    >  2:111909/1‑141 (MQ=255)                         aaCAAAAATAAAAGCAATAAGATAATCATAGTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAaatataata                                                                                                              <  2:283239/141‑1 (MQ=255)                                           aaGATAATCATATTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACtttgttt                                                                                            <  1:76150/141‑1 (MQ=255)                                                       tttCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTg                                                                                <  1:107545/141‑1 (MQ=255)                                                                  aaaGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTTGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTAtt                                                                     <  2:104509/141‑1 (MQ=255)                                                                                     aTAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAATTATTTGctctctt                                                  >  2:108993/1‑140 (MQ=255)                                                                                             atatatTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACaa                                          <  1:111909/141‑1 (MQ=255)                                                                                             atatatTAATTTAGGTGGTTGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTATCTTATTTTTAAATATGTGCTCACTATATGACaa                                          <  2:300142/141‑1 (MQ=255)                                                                                                tatttattTAGGTGGTGGTCCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATaa                                       <  1:43642/141‑1 (MQ=255)                                                                                                  tgtctttaGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATGTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAg                                     <  1:212523/137‑1 (MQ=255)                                                                                                        taGGTGGTGGTTCATTCTTTACTATTTATATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTATATATAGTCTCACTATATGACAATAAAGTTCAtt                               >  2:210731/1‑140 (MQ=255)                                                                                                        taGGTGGTGGTTCATTCTTTACTATTTACATGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAGTTCATg                               <  2:173739/141‑1 (MQ=255)                                                                                                                                     atGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAATTTCATGTATGATTTAAATCAAATGGAATTGAAAAg  <  2:179264/141‑1 (MQ=255)                                                                                                                                     atGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAGTTCATGTATTATTTAAATCAAATGGAATTGAAAAg  <  2:237357/141‑1 (MQ=255)                                                                                                                                     atGTTAATGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAGTTCATGTATTATTTAAATCAAATGGAATTGAAAAg  <  2:244113/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                       TTAAAGTTACAAATCTATAATGAAAACAAAAATAAAAGCAATAAGATAATCATATTTCCCACTTTAAAGAGTCTTTGTTTATCAATAGTTTTATATATTTATTTAGGTGGTGGTTCATTCTTTACTATTTATATGTTATTGACGATTGAAGTTCAAAATATAATATTATTTATAACTTTGTTTGTAATATTTTTGTTTTTCTTATTTTTAAATATGTGCTCACTATATGACAATAAAGTTCATGTATTATTTAAATCAAATGGAATTGAAAAG  >  USA300TCH1516_ALE/661222‑661494

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: ‑