Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	920,568	G→A	intergenic (+197/‑16)	USA300HOU_RS04555 → / → USA300HOU_RS04565	Putative monooxygenase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	920,568	0	G	A	100.0%	59.6 / NA	17	intergenic (+197/‑16)	USA300HOU_RS04555/USA300HOU_RS04565	Putative monooxygenase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (12/5);  total (12/5)

CCAATTTAATCAAACGAAAACATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATGACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCGAATTAGATGCGACATAC  >  USA300TCH1516_ALE/920454‑920709                                                                                                                   |                                                                                                                                              ccAATTTAATCAAACGAAAACATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTaa                                                                                                             >  2:11311/1‑149 (MQ=255)              aCGAAAACATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGa                                                                                                >  1:166736/1‑149 (MQ=255)              aCGAAAACATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGa                                                                                                >  1:58411/1‑149 (MQ=255)                     cATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTAt                                                                                         <  1:46886/149‑1 (MQ=255)                            cTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATtat                                                                                  >  2:165500/1‑149 (MQ=255)                                       cGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTa                                                                       >  1:32659/1‑149 (MQ=255)                                       cGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTa                                                                       >  2:172475/1‑149 (MQ=255)                                                      aaGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACCTTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGAt                                                        <  1:258594/149‑1 (MQ=255)                                                       aGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATa                                                       >  1:183540/1‑149 (MQ=255)                                                        gCAAAAACATCAAACTAAAGATCGCTGAAATGATTATGATAAAAGTTATATGGTAAGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGATGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATaa                                                      >  1:49553/1‑149 (MQ=255)                                                                          aGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTgg                                    >  1:171667/1‑149 (MQ=255)                                                                                           aTGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCg                   >  1:47010/1‑149 (MQ=255)                                                                                           aTGATAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCg                   >  1:47075/1‑149 (MQ=255)                                                                                              aTAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTTATACATATGCTGGACATTTTCCGGTTGTCGAAt                <  2:253805/149‑1 (MQ=255)                                                                                               tAAAAGTTATATGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCGAAtt               >  1:261573/1‑149 (MQ=255)                                                                                                       atatGGTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCGAATTAGATGCGa       <  1:103223/149‑1 (MQ=255)                                                                                                            gTATGATAACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCGAATTAGATGCGACATAc  <  1:35050/149‑1 (MQ=255)                                                                                                                   |                                                                                                                                              CCAATTTAATCAAACGAAAACATCAAGCTGAAGATCGCCGAAAGATTTTAATCAAGCAAAAACATCAAACTAAAGTTCGCTGAAATGATTATGATAAAAGTTATATGGTATGATGACATTGGTGATATATATGATAAACATCGGATTAACAGGTTGGGGTGATCACTATTCATTATATGAAGATTTAGAACGCCAAACCGATAAACTTAAAACATATGCTGGACATTTTCCGGTTGTCGAATTAGATGCGACATAC  >  USA300TCH1516_ALE/920454‑920709

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑