Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,758,882	G→A	Q138* (CAA→TAA)	USA300HOU_RS08780 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,758,882	0	G	A	100.0%	104.9 / NA	29	Q138* (CAA→TAA)	USA300HOU_RS08780	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/15);  total (14/15)

TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  USA300TCH1516_ALE/1758746‑1759013                                                                                                                                         |                                                                                                                                    tttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACAtt                                                                                                                                 >  2:195063/1‑141 (MQ=255)  ttGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACAttt                                                                                                                                >  2:287166/1‑141 (MQ=255)     aaCTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCaa                                                                                                                             >  1:64096/1‑141 (MQ=255)               aCCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGCTAAGCATTTTCAGATTTTAGTTGTACAATTTCCCTTGCTTCATTTAAGTCTTGTTACATTTCAAATTCAGTAtt                                                                                                                   >  1:2621/1‑141 (MQ=255)                ccTTTTAAATTTATTCTAGTGACAGGATAACTAAAATTTATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTg                                                                                                                  <  2:208145/141‑1 (MQ=255)                ccTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTg                                                                                                                  <  1:199256/141‑1 (MQ=255)                                         gATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCaa                                                                                         <  2:95192/141‑1 (MQ=255)                                             aCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAAttt                                                                                     >  1:158902/1‑141 (MQ=255)                                             aCTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAAttt                                                                                     >  2:205453/1‑141 (MQ=255)                                                     atatTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGaa                                                                             <  2:64096/141‑1 (MQ=255)                                                        tttCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATaa                                                                          >  1:24870/1‑141 (MQ=255)                                                          tCTTATGCAATAATGTCCTATTCGAAAGCAAATTCATATTTAATTTGGAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAAt                                                                        <  1:83289/141‑1 (MQ=255)                                                                gCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGtct                                                                  <  1:235827/141‑1 (MQ=255)                                                                gCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGtct                                                                  <  1:50442/141‑1 (MQ=255)                                                                    taatTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTctcctc                                                              <  1:253334/141‑1 (MQ=255)                                                                    taatTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTctcctc                                                              <  2:226768/141‑1 (MQ=255)                                                                           cTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGAcc                                                       >  1:53442/1‑141 (MQ=255)                                                                           cTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCACTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGAcc                                                       >  2:247551/1‑141 (MQ=255)                                                                                  tAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATATTCAATCTGATAAAGAATAAATTCGTCTCCTCTTTGACCTataata                                                <  1:209834/141‑1 (MQ=255)                                                                                   aaGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAatat                                               <  1:9356/141‑1 (MQ=255)                                                                                         tttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGAt                                         >  1:1736/1‑141 (MQ=255)                                                                                          ttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATc                                        <  2:158902/141‑1 (MQ=255)                                                                                          ttCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATc                                        <  1:205453/141‑1 (MQ=255)                                                                                            cAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTTACGCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCAt                                      >  1:56805/1‑141 (MQ=255)                                                                                            cAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCAt                                      >  1:65197/1‑141 (MQ=255)                                                                                                  ttttttGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGTCTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAg                                >  2:213579/5‑141 (MQ=255)                                                                                                                              tAAGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCAt    <  1:195063/141‑1 (MQ=255)                                                                                                                               aaGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATa   <  1:287166/141‑1 (MQ=255)                                                                                                                                aGTCTTGTTACATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATaa  >  2:255330/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                    TTTGAACTACACCAACCTTTTAAATTTATTCTAGTGACAGGATAACTAAAATATATTTCTTATGCAATAATTTCCTATTGATAAGCATTTTCAGATTTTAGTTGTAAATTTTGCCCTAATTCATTTAAGTCTTGTTGCATTTCAAATTCAGTATTGTAAACACGCATTGACTCATCTCCAAATTTATAAAGAATAAATTCGTCTCCTCTTTGACCTATAATATATTGATCATTATAAGCCATGCGATTCATTCCAGACACAGCCATAA  >  USA300TCH1516_ALE/1758746‑1759013

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: ‑