Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,652	C→T	intergenic (‑8/+7)	USA300HOU_RS10230 ← / ← USA300HOU_RS10235	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,652	0	C	T	100.0%	83.9 / NA	25	intergenic (‑8/+7)	USA300HOU_RS10230/USA300HOU_RS10235	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/11);  total (14/11)

CACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAACTCTGATTT  >  USA300TCH1516_ALE/2028521‑2028787                                                                                                                                     |                                                                                                                                        cacaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTa                                                                                                                                >  1:84494/1‑141 (MQ=255)     tCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGcc                                                                                                                            <  1:262735/141‑1 (MQ=255)       ccAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTTCCTTTCTATGCcac                                                                                                                          >  1:121859/1‑141 (MQ=255)       ccAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCcac                                                                                                                          >  1:130996/1‑141 (MQ=255)        cAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCcaca                                                                                                                         >  1:98224/1‑141 (MQ=255)                 aaCGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCCATTGTCTGCTATGCCACAGCGTTCata                                                                                                                <  1:119776/141‑1 (MQ=255)                      gTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAAtt                                                                                                           <  1:89826/141‑1 (MQ=255)                        aaaaaGCCAATTTTTTCAAACAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAAtttt                                                                                                         >  1:304868/1‑140 (MQ=255)                        aaaaaGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATtta                                                                                                         >  1:163250/1‑141 (MQ=255)                                         aaaaaaTATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGttttt                                                                                        >  1:16955/1‑141 (MQ=255)                                                  gtagtaAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCGTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCt                                                                               <  1:42353/141‑1 (MQ=255)                                                        aaaaTTGGCAATAATCCTTAAGTGTTG‑AAAAAGGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTAttttt                                                                         <  1:212447/141‑1 (MQ=255)                                                                  ataatCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAg                                                               <  1:264672/141‑1 (MQ=255)                                                                   taatCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTGTTTCTGTTGCTATTTTTTCAGTTGAAGt                                                              <  1:317567/141‑1 (MQ=255)                                                                                   tAAAAATTGTCAACCTTGGCGTGGATATTTATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               <  1:108296/141‑1 (MQ=255)                                                                                   tAAAAATGATCAACATTTGCGTTGATATCTATTTGTGTGTCCTGTTGCGCTGCCTTTCTATGCCACCACGTATAAATATTTTCTTCGACGCTTTGGTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               <  1:366481/141‑1 (MQ=255)                                                                                   tAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               >  1:177849/1‑141 (MQ=255)                                                                                      aaaTGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTc                                            >  1:106426/1‑141 (MQ=255)                                                                                      aaaTGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTc                                            >  1:157727/1‑141 (MQ=255)                                                                                          gATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAAtt                                        >  1:387144/1‑141 (MQ=255)                                                                                          gATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAAtt                                        >  1:188175/1‑141 (MQ=255)                                                                                            tCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTtg                                      >  1:27229/1‑141 (MQ=255)                                                                                                 aTTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGCTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCat                                 <  1:331093/141‑1 (MQ=255)                                                                                                        ttGATATATATTTGTGTGTCATATTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGATTGTTGAATTTGAGTTTCAATTTGTGCATAATATGc                          <  1:346426/141‑1 (MQ=255)                                                                                                                           cATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAActct       >  1:281270/1‑141 (MQ=255)                                                                                                                                tccgctgcCTTTCTATGCCACGTCTTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTCTATTCAACTCTGAttt  <  1:256391/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                        CACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAACTCTGATTT  >  USA300TCH1516_ALE/2028521‑2028787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑