Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	665,392	T→G	L79* (TTA→TGA)	paiA_1 →	Spermidine/spermine N(1)‑acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	665,392	0	T	G	100.0%	196.5 / NA	56	L79* (TTA→TGA)	paiA_1	Spermidine/spermine N(1)‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (29/27);  total (29/27)

CGACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATGAAGAAGCAG  >  USA300TCH1516_ALE/665254‑665532                                                                                                                                           |                                                                                                                                             cGACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATNGTTGGCTTTGCTAACTTTATTTCCGGTGAAGAATgat                                                                                                                                            >  2:656142/1‑141 (MQ=255) cGACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATgat                                                                                                                                            >  2:260454/1‑141 (MQ=255) cGACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATgat                                                                                                                                            >  1:353980/1‑141 (MQ=255)  gACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATgata                                                                                                                                           >  2:530724/1‑141 (MQ=255)  gACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGGAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATgata                                                                                                                                           >  1:595315/1‑141 (MQ=255)   acaacaGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGatat                                                                                                                                          >  1:924392/1‑141 (MQ=255)      acaGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATAtttt                                                                                                                                       >  1:764675/1‑140 (MQ=255)      acaGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTa                                                                                                                                       <  1:152409/141‑1 (MQ=255)           tAATCACTTGTTAGAATCATCATATAATTAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGc                                                                                                                                  <  2:396363/141‑1 (MQ=255)               cACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCAt                                                                                                                              <  1:840273/141‑1 (MQ=255)                         aaGCTTCAAATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAAc                                                                                                                    <  1:509096/141‑1 (MQ=255)                             ttCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTATGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGa                                                                                                                >  2:873952/1‑141 (MQ=255)                             ttCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCTGCTCATTATGTTAAACCAGa                                                                                                                >  2:785157/1‑141 (MQ=255)                               cATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAAACAGAAt                                                                                                              >  1:116085/1‑141 (MQ=255)                                  ataATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTCGTAGTTGAAGAAGGTAATGACATGGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGc                                                                                                           >  2:93/1‑141 (MQ=255)                                   taATGAACATCATTTAAAGAAAGGACTTCAAGAACACTTATTCTTAGTCGTTGAGGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCGTTATGTTACACCAGAATCGCa                                                                                                          >  2:286257/1‑141 (MQ=255)                                      tGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACa                                                                                                       >  1:894807/1‑141 (MQ=255)                                            tcatTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAgg                                                                                                 >  2:888769/1‑141 (MQ=255)                                              atTTAAAGAAAAGACTTCAAGAACAATTATTCTTACTCGTTGAGGAAGGTAATGACATCGTTGGATTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCATCTGATTATGTTAAACAAGACTCGCCACATACAGAtt                                                                                               >  2:152359/1‑141 (MQ=255)                                               tttAAAGAAAAGACTACAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATCTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTa                                                                                              <  2:813798/141‑1 (MQ=255)                                                ttAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCCTTATGTTAAACAAGAATCGCAACATACaagggag                                                                                             >  2:868255/1‑135 (MQ=255)                                                ttAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACCGGTTAt                                                                                             >  2:269493/1‑141 (MQ=255)                                                  aaagaaaagaCTTCAAGAACAATTATTTTTAGTCGTTGAAGAAGGGAATGACATCGTTGGCTTTGTTAATTTTATTTACGGTGAAGAATGATATGTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATgg                                                                                           <  2:317819/141‑1 (MQ=255)                                                    agaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTa                                                                                         >  1:489193/1‑141 (MQ=255)                                                        aagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGc                                                                                     >  1:239639/1‑141 (MQ=255)                                                        aagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTAAAGc                                                                                     >  1:239848/1‑141 (MQ=255)                                                             ttCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATGGt                                                                                >  2:436466/1‑141 (MQ=255)                                                              tCAAGAACAATTATTCTTAGTCGTGGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTCTCAGTTCATTATGTTAAACCAGAATCGCAGAATACACGTCATGATAACGCATTGtt                                                                               >  2:635874/1‑141 (MQ=255)                                                               cAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTa                                                                              >  2:873237/1‑141 (MQ=255)                                                                 aGAACAATTATTTTTAGTCGTTGAAGAAGTTAACGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTACTAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTaaa                                                                            <  1:228768/141‑1 (MQ=255)                                                                 aGAACAATTAGTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTGATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTaaa                                                                            <  2:398701/141‑1 (MQ=255)                                                                 aGAACAATTAGTCTTACTGGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTaaa                                                                            <  1:923513/141‑1 (MQ=255)                                                                  gAACAATTATTCTTAGTCGTTGAAGAAGGGAATGACATCGTTGGATTTGCTAACTTTATTTACGGTGAAGAATGATATCTAGCAGCTCATTATGTTACATCAGAAACGCAACCTACAGGTTATGGTACAGCGTTGTTaaag                                                                           >  2:358389/1‑140 (MQ=255)                                                                     cAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTAAAGCATTGTTAAATGaa                                                                        >  2:23725/1‑141 (MQ=255)                                                                             cTTAGTCGTTGACGAAGGTAATGACATCGTTGGGTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTAGGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATc                                                                <  2:515303/141‑1 (MQ=255)                                                                                     ttGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                        <  2:904113/141‑1 (MQ=255)                                                                                     ttGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                        <  1:569034/141‑1 (MQ=255)                                                                                     ttGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                        <  1:222193/141‑1 (MQ=255)                                                                                      tGAAGCAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCCACATACAGGTTATGTTACAGCCTCGTTAACAGAAGGATTATCACGTTTTGa                                                       >  2:169857/1‑141 (MQ=255)                                                                                              gTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAt                                               <  1:696446/141‑1 (MQ=255)                                                                                               tAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGCTATGGTACAGCATTGTTAAATGAAGGATTATCCCGTTTTGCAGATAAAtt                                              <  2:678196/141‑1 (MQ=255)                                                                                                aaTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                             <  1:919978/141‑1 (MQ=255)                                                                                                aaTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                             <  1:334849/141‑1 (MQ=255)                                                                                                aaTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                             <  2:595315/141‑1 (MQ=255)                                                                                                aaTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                             <  1:312750/141‑1 (MQ=255)                                                                                                aaTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                             <  1:63530/141‑1 (MQ=255)                                                                                                 aTGACATCGTTGGCTTTGCTAACTTTATTTACGATGAAGAATGATGTTTATCATCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTg                                            >  1:875464/1‑141 (MQ=255)                                                                                                   taaaacGTTGGCTTTGCTATCGTTATGTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCAGTTTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGaa                                          <  1:87720/136‑1 (MQ=255)                                                                                                   taCATCTTTGGCTTTGCTAAGTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGaa                                          <  2:392384/140‑1 (MQ=255)                                                                                                   gACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTGGAAGATAAATTTGaa                                          <  1:685021/141‑1 (MQ=255)                                                                                                              ttttGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACtt                               <  2:669997/140‑1 (MQ=255)                                                                                                              cTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACtt                               <  2:720545/141‑1 (MQ=255)                                                                                                               tttGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCACCATACAGGTTATGGTACAGCATTGTTAAAGGACGGATTATAACGTTTGGAAGATAAATTTGAAGGTGTGTCCTTa                              >  1:434676/1‑141 (MQ=255)                                                                                                                    tAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGt                         <  1:873237/141‑1 (MQ=255)                                                                                                                           atttaCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGatact                  >  1:357919/1‑139 (MQ=255)                                                                                                                           atttaCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATCATCACGTTTTGAGGATAAAGTGGAGGGTGTTTACTGTGAAGTAGttaat                  >  1:227427/1‑141 (MQ=255)                                                                                                                              taCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGCGGTAGATAATaaa               >  2:433443/1‑141 (MQ=255)                                                                                                                                cGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTCGAAGTAGAAAATaaaaa             >  1:196269/1‑141 (MQ=255)                                                                                                                                cGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATaaaaa             >  2:655446/1‑141 (MQ=255)                                                                                                                                cGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGGGTTTACTTAGAAGTAGATAATaaaaa             >  2:811187/1‑141 (MQ=255)                                                                                                                                      agaaTGATATTTATCAGCCCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATgaaga       <  2:485826/141‑1 (MQ=255)                                                                                                                                        aagtataTTTAGCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATGaagaag     <  2:744039/138‑1 (MQ=255)                                                                                                                                           tataGTTACCATCTCATTATTTTAAACCACAATCGCAACATACAGTTTATGGTACAGCATTGTTAAATGAAGGACTAACACCCTTTGAAGATAAATTGGAAGGTGTTTACTTAGAAGTAGATAATAAAAATCAAGAAGCAg  <  2:280190/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                             CGACAACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATGAAGAAGCAG  >  USA300TCH1516_ALE/665254‑665532

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑