Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	76,236	C→T	Q233* (CAA→TAA)	USA300HOU_RS00140 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	76,236	0	C	T	100.0%	59.8 / NA	25	Q233* (CAA→TAA)	USA300HOU_RS00140	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (11/14);  total (11/14)

AGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTTCATCATTCAACGGTCTACCGTT  >  USA300TCH1516_ALE/76101‑76362                                                                                                                                        |                                                                                                                               aGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGACCTATTTCAGATATAAATAAtt                                                                                                                            >  2:214433/1‑140 (MQ=255)      tCCAGGGAATACTAACACAAAGGCAATGAATTTAATAATGATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACa                                                                                                                       <  1:90521/140‑1 (MQ=255)        cAGGGAATACTAACATAAAGAAAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTAAAATATAAAAAAAAAAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAg                                                                                                                     <  2:129967/140‑1 (MQ=18)                        aaaGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAg                                                                                                     <  2:68802/140‑1 (MQ=255)                              aggtaatttagtAATTAGAGCAAAATATAGGTTCTGTTGCAAAGTTGAATGTATAGTATAATTTTAACAAAAAGGAGTCTGCTGTATGAACTATTTCAGATATAACTAATTTAACAAGGATGTTATCACTGTAGCCGTTg                                                                                               <  2:141158/137‑1 (MQ=14)                                   atttaatAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTACCAAGGATGTTATCACTGTAGCCGTTGGctac                                                                                          <  1:74434/140‑1 (MQ=255)                                   atttaatAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGctac                                                                                          <  1:225663/140‑1 (MQ=255)                                   aattaatAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGctac                                                                                          <  1:157520/138‑1 (MQ=255)                                                       gataGATTATATTGCAAAGGTGAATATATAGTAAAAAAAAAAAAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAg                                                                      <  2:121294/139‑1 (MQ=11)                                                          aGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTa                                                                   >  2:75742/1‑140 (MQ=21)                                                                  ttGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGata                                                           >  1:182837/1‑140 (MQ=21)                                                                  gtGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGGCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGata                                                           <  1:210606/139‑1 (MQ=19)                                                                     cAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTTGGAGGCATTTTAGCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGatatat                                                        >  1:192073/1‑140 (MQ=11)                                                                      aaaGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGatatatt                                                       >  1:207620/1‑139 (MQ=37)                                                                           tGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGaaa                                                  >  1:209473/1‑140 (MQ=37)                                                                                 tataGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTaa                                            <  1:228631/140‑1 (MQ=18)                                                                                        taATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACg                                     <  1:250163/140‑1 (MQ=18)                                                                                               aaCAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTa                              <  2:69252/140‑1 (MQ=17)                                                                                                    aaaGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGTGAACGTGGTGTAAACGt                         >  2:22559/1‑140 (MQ=12)                                                                                                    aaaGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTACACGt                         >  2:22558/1‑140 (MQ=12)                                                                                                      aGGAGTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTtc                       >  1:121160/1‑140 (MQ=17)                                                                                                          gTCTTCTGTATGAACTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTtcatca                   >  1:223773/1‑140 (MQ=18)                                                                                                                      aaCTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTTCATCATTCAACGGTCTa       >  1:108234/1‑140 (MQ=18)                                                                                                                       aCTATTTCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTTCATCATTCAACGGtagac      <  1:156756/140‑5 (MQ=12)                                                                                                                           tttCAGATATAAATAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTTCATCATTCAACGGTCTACCGtt  <  1:72490/140‑1 (MQ=17)                                                                                                                                        |                                                                                                                               AGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTAAACGTTCATCATTCAACGGTCTACCGTT  >  USA300TCH1516_ALE/76101‑76362

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: ‑