Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,664,466	G→A	A65T (GCG→ACG)	pitA_2 →	L‑methionine sulfoximine/L‑methionine sulfone acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,664,466	0	G	A	100.0%	184.7 / NA	50	A65T (GCG→ACG)	pitA_2	L‑methionine sulfoximine/L‑methionine sulfone acetyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (21/29);  total (21/29)

ATGCCATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTGCGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCAAAAGCTAAAGGTTA  >  USA300TCH1516_ALE/2664329‑2664608                                                                                                                                          |                                                                                                                                               atgCCATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCgg                                                                                                                                      <  1:37189/148‑1 (MQ=255) atgCCATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCgg                                                                                                                                      <  1:145416/148‑1 (MQ=255) atgCCATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCgg                                                                                                                                      <  1:82148/148‑1 (MQ=255)     cATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCa                                                                                                                                  <  1:251342/148‑1 (MQ=255)              tactacAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCt                                                                                                                         >  1:165159/1‑148 (MQ=255)              tactacAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCt                                                                                                                         >  1:165278/1‑148 (MQ=255)              tactacAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCt                                                                                                                         >  2:228053/1‑148 (MQ=255)              tactacAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCt                                                                                                                         >  2:11446/1‑148 (MQ=255)              tactacAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGGCTTAGGGTTTACGACGTTCGGTTCATTTAGACCt                                                                                                                         >  1:133088/1‑148 (MQ=255)                       tGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCa                                                                                                                <  1:263196/148‑1 (MQ=255)                       tGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCa                                                                                                                <  2:186941/148‑1 (MQ=255)                            ataCTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGAGCTTGGCCAGCATACCt                                                                                                           <  1:336273/148‑1 (MQ=255)                            ataCTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCt                                                                                                           <  2:334873/148‑1 (MQ=255)                             taCTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCta                                                                                                          <  2:36883/148‑1 (MQ=255)                                   tGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACa                                                                                                    >  2:50602/1‑148 (MQ=255)                                       ccACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCg                                                                                                >  1:166131/1‑148 (MQ=255)                                       ccACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCg                                                                                                >  2:343050/1‑148 (MQ=255)                                            aaCCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACAt                                                                                           <  2:337766/148‑1 (MQ=255)                                            aaCCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACAt                                                                                           <  2:92293/148‑1 (MQ=255)                                            aaCCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACAt                                                                                           <  1:331546/148‑1 (MQ=255)                                                    aCGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTa                                                                                   >  2:379746/1‑148 (MQ=255)                                                             tCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGc                                                                          <  2:71833/148‑1 (MQ=255)                                                                 aTGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCttaa                                                                      >  1:16201/1‑146 (MQ=255)                                                                 aTGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCa                                                                      >  2:146989/1‑148 (MQ=255)                                                                 aTGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCa                                                                      >  1:14414/1‑148 (MQ=255)                                                                 aTGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCa                                                                      >  2:128739/1‑148 (MQ=255)                                                                 aTGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTACTCATGTCGATGATTCa                                                                      >  1:213993/1‑148 (MQ=255)                                                                     tttGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTa                                                                  <  2:24849/148‑1 (MQ=255)                                                                           acgaaacAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGaa                                                            >  2:81009/1‑148 (MQ=255)                                                                           acgaaacAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGaa                                                            >  2:141942/1‑148 (MQ=255)                                                                              aaacAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAg                                                         <  1:195566/148‑1 (MQ=255)                                                                              aaacAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAg                                                         <  2:311863/148‑1 (MQ=255)                                                                                acaacGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGt                                                       <  2:213583/148‑1 (MQ=255)                                                                                acaacGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGt                                                       <  1:370522/148‑1 (MQ=255)                                                                                     gTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGc                                                  <  1:102744/148‑1 (MQ=255)                                                                                     gTAAGCATGAGACTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAAAAAAAAAAAAAGGTATTGc                                                  <  2:86342/148‑1 (MQ=255)                                                                                         gCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGt                                              >  1:65038/1‑148 (MQ=255)                                                                                              aGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAAtt                                         <  1:109923/148‑1 (MQ=255)                                                                                               gCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATta                                        >  2:333641/1‑148 (MQ=255)                                                                                                ccTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATtac                                       <  1:343050/148‑1 (MQ=255)                                                                                                  tATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATtacta                                     <  1:101274/148‑1 (MQ=255)                                                                                                  tATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATtacta                                     <  1:341725/148‑1 (MQ=255)                                                                                                              tGAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAAtt                         >  2:240055/1‑148 (MQ=255)                                                                                                               gAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATtg                        <  2:294301/148‑1 (MQ=255)                                                                                                               gAGGAAAATGGAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATtg                        <  2:122510/148‑1 (MQ=255)                                                                                                                        ggAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCaa               <  2:310999/148‑1 (MQ=255)                                                                                                                        ggAAGTGTCTTAGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCaa               <  2:143061/148‑1 (MQ=255)                                                                                                                                   aGGGTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCAAAAGCTAAAGGt    >  1:18824/1‑148 (MQ=255)                                                                                                                                     ggTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCAAAAGCTAAAGGTTa  >  1:200245/1‑148 (MQ=255)                                                                                                                                     ggTTTACGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCAAAAGCTAAAGGTTa  <  1:379746/148‑1 (MQ=255)                                                                                                                                          |                                                                                                                                               ATGCCATTATCAATACTACAGCTGTTTATACTTATGAACCACAAACCATAGACGAACGTGTCGCATGGTTTGAAACGAAACAACGTAAGCATGAGCCTATCTTTGTATTTGAGGAAAATGGAAGTGTCTTAGGGTTTGCGACGTTCGGTTCATTTAGACCTTGGCCAGCATACCTATATACAATCGAACATTCTATTTATGTCGATGCTTCAGCTAGAGGAAAAGGTATTGCTAGTCAATTACTACACCATTTAATTGTGGAAGCAAAAGCTAAAGGTTA  >  USA300TCH1516_ALE/2664329‑2664608

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑