Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	973,213	C→A	E175* (GAG→TAG)	yitU_1 ←	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	973,213	0	C	A	100.0%	123.6 / NA	44	E175* (GAG→TAG)	yitU_1	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/16);  total (28/16)

CACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGAT  >  USA300TCH1516_ALE/973084‑973344                                                                                                                                  |                                                                                                                                    caCCGAATGCAATAATATTATTTAAGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTCACAAATTCAATGACAGGGAATGGTGCGCCGCAGCGTCGATGATAAatat                                                                                                                                >  1:165803/1‑135 (MQ=255)     gtaTGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATc                                                                                                                            <  2:649019/133‑1 (MQ=255)        tGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGc                                                                                                                         >  2:599215/1‑135 (MQ=255)         gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                        >  1:334717/1‑135 (MQ=255)          cAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCAt                                                                                                                       >  2:209584/1‑135 (MQ=255)          cAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCAt                                                                                                                       <  1:523840/135‑1 (MQ=255)                         ggTCAATATTTGAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCa                                                                                                        <  1:23168/135‑1 (MQ=255)                         ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTATTAACAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGACGATGCTAAACATGATCGGCATAAAAACGAGTAAGCa                                                                                                        >  2:23646/1‑135 (MQ=255)                          gTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCat                                                                                                       <  1:440165/135‑1 (MQ=255)                                  ttAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGa                                                                                               <  2:653078/135‑1 (MQ=255)                                     aaaaTTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAttt                                                                                            >  1:446251/1‑135 (MQ=255)                                         ttGTCTAACTTGCTCAATGCCTCTTCCTTTATTAATACCAAGTTTTACTATTTCAATGACAGGGAATGATGCGCCCCAGCGTCGATGCTAAATATAATCGGCATAAAAATGAGTAAGCATATTTTTGAtttacgg                                                                                        >  2:350498/1‑131 (MQ=255)                                               aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAtttt                                                                                  >  2:254014/1‑135 (MQ=255)                                               aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAtttt                                                                                  >  2:141322/1‑135 (MQ=255)                                               aaCTTGCTCAATGCATCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAAAGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGAATATTTTTGATTTCAGGTAtttt                                                                                  >  2:128487/1‑135 (MQ=255)                                                aCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                 <  2:49281/135‑1 (MQ=255)                                                     cTCAATGCCTCTTGCTTTATTAATACCAAATATTAAAATTTCAATGACAGGGAATGGAGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTGACTttc                                                                            >  1:20193/1‑135 (MQ=255)                                                           gCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGc                                                                      >  2:576755/1‑135 (MQ=255)                                                             ctctTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTTTTCGGCtt                                                                    >  1:57155/1‑135 (MQ=255)                                                                ttGCTTTATTAATACCAAGTTTTACAATTAAAATGACAGGAAAAGGTTCGAACAAGGTTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCAGATTTTTGATTTCAGCTATTTTACATTCTTCGGCTTcga                                                                 >  2:592095/1‑133 (MQ=255)                                                                   cTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTa                                                              >  2:573686/1‑135 (MQ=255)                                                                   cTTTATTAATACCAAGTTTTACAAATTAAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTa                                                              >  1:8316/1‑135 (MQ=255)                                                                   cTTTATTAATACCAAGTTTAACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTa                                                              >  1:631238/1‑135 (MQ=255)                                                                      tattcATACCAAGTTTTACAATTTCAATAACAGGGAATAGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTTCTTTCTTCGGCTTCAATTaaaa                                                           >  1:142907/1‑135 (MQ=255)                                                                              ccAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGTTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTa                                                   <  2:14047/135‑1 (MQ=255)                                                                                  gTTTTACAATTTCAATGACAAGGAATGATGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTCAAATTGAGGTAgggg                                               >  1:336739/1‑135 (MQ=255)                                                                                   ttttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCTGCTTCAATTAAAATTGAGGTAGGGGa                                              <  1:588672/135‑1 (MQ=255)                                                                                     ttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGAtt                                            >  2:606866/1‑135 (MQ=255)                                                                                     ttACAATTTCAATGACAGGGAATAGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGAtt                                            >  1:43945/1‑135 (MQ=255)                                                                                            ttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                     <  1:647104/135‑1 (MQ=255)                                                                                            ttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                     >  2:162032/1‑135 (MQ=255)                                                                                            ttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                     <  2:509735/135‑1 (MQ=255)                                                                                                 tGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTTAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGa                                <  1:256916/135‑1 (MQ=255)                                                                                                    cAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGTTTTCTTGTATTTGACTTTCTTCGGCAGCAATTAAAATTGAGTTAGGGGATTTTTTGAGGTggtaaa                             >  2:235031/1‑131 (MQ=255)                                                                                                     aGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAg                            >  2:300556/1‑135 (MQ=255)                                                                                                     aGGGAATGGTGCGCCCAAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTACGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTCAGGTAGGTGATTCTTTAAAGTGGAAAAg                            >  2:383431/1‑135 (MQ=255)                                                                                                     aGGGAATGGTGCGCACCAGCGTAGATGCTAAATTTGATTGGCACCTGGAGGATAAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAg                            <  1:23646/135‑1 (MQ=255)                                                                                                             gTGCGCCCCAGCGTCGATGCTAAATATCATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAGTTGAGGTATGTGATTCTTTTAAGTGGACAAGTAAATTAc                    <  1:316944/135‑1 (MQ=255)                                                                                                                 gcCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGATGTAGGGGATTTTTTCAAGTTGACAAGTAAATTACCAGt                <  1:162032/135‑1 (MQ=255)                                                                                                                    ccAGCGTCGATGATAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCAGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTg             >  2:441998/1‑135 (MQ=255)                                                                                                                          tCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATCTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGCTAACGTAAAGTACCAGTTTGAATACt       >  2:423786/1‑135 (MQ=255)                                                                                                                            gATGCTAAATATGATAAGCATAAAAATGAGTAAGAATATTTTTGATTTAAGGTATTATAAATTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTAAAGTGGACAAGTAAATTACCAGTTTGAGttgttg     >  1:332481/1‑135 (MQ=255)                                                                                                                             aTGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTgg    <  1:213658/135‑1 (MQ=255)                                                                                                                               gCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGAt  <  2:12486/135‑1 (MQ=255)                                                                                                                                  |                                                                                                                                    CACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGAT  >  USA300TCH1516_ALE/973084‑973344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑