Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	58,444	G→T	intergenic (+890/+27)	USA300HOU_RS00240 → / ← USA300TCH1516_00049	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	58,444	0	G	T	100.0%	86.4 / NA	25	intergenic (+890/+27)	USA300HOU_RS00240/USA300TCH1516_00049	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (13/12);  total (13/12)

CTTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACTTTT  >  USA300TCH1516_ALE/58306‑58580                                                                                                                                           |                                                                                                                                         ctTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACatat                                                                                                                                        >  1:89529/1‑141 (MQ=255)  tttttAAAATCATCTAGTATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGTCTGGAAATTCAATGCTGTAAAATTAGACATAtt                                                                                                                                       >  1:296957/1‑141 (MQ=255)   ttttAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAttt                                                                                                                                      >  1:400792/1‑141 (MQ=255)   ttttAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAttt                                                                                                                                      >  1:32400/1‑141 (MQ=255)             atcTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAagta                                                                                                                            >  1:133549/1‑141 (MQ=255)                        tatataATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAg                                                                                                                 <  1:320164/141‑1 (MQ=255)                               ttCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAGTTTAAAAAAGTAGTAATAAAAAGTCTAAGt                                                                                                          >  1:82052/1‑141 (MQ=255)                                             gtaTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaat                                                                                            <  1:317477/141‑1 (MQ=255)                                               aTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:108959/141‑1 (MQ=255)                                               aTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:439998/141‑1 (MQ=255)                                               aTTAACCTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:108784/141‑1 (MQ=255)                                                 tAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAAc                                                                                        >  1:383236/1‑141 (MQ=255)                                                 tAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAAc                                                                                        >  1:231675/1‑141 (MQ=255)                                                     gTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTca                                                                                    >  1:501996/1‑140 (MQ=255)                                                                        aaaTATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAAGTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAaaataaat                                                                 <  1:36825/141‑1 (MQ=255)                                                                            atTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAGTAAATATGa                                                             >  1:6671/1‑141 (MQ=255)                                                                                          tAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATCTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAtttt                                               <  1:360237/141‑1 (MQ=255)                                                                                                ttgaaaTTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCCTTTAATTTCTataa                                         <  1:272809/138‑1 (MQ=255)                                                                                                        ataCGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAATGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAg                                 <  1:199651/141‑1 (MQ=255)                                                                                                        ataCGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAg                                 >  1:284859/1‑141 (MQ=255)                                                                                                                   aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGa                      >  1:243441/1‑141 (MQ=255)                                                                                                                   aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGa                      >  1:462212/1‑141 (MQ=255)                                                                                                                     tttaaTGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGAtt                    <  1:472761/138‑1 (MQ=255)                                                                                                                     ttCAATGCTTTAAAAATAGACATATTTTAAAAAAGTAGTAATAAATAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGAtt                    <  1:467867/141‑1 (MQ=255)                                                                                                                               tAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTg          <  1:78168/141‑1 (MQ=255)                                                                                                                                       gACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACtttt  >  1:454599/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                         CTTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACTTTT  >  USA300TCH1516_ALE/58306‑58580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑