Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,750,562	T→C	V197V (GTA→GTG)	betA ←	Oxygen‑dependent choline dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,750,562	0	T	C	100.0%	217.4 / NA	57	V197V (GTA→GTG)	betA	Oxygen‑dependent choline dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/39);  total (18/39)

TTTTTCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGTACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTAATT  >  USA300TCH1516_ALE/2750419‑2750700                                                                                                                                                |                                                                                                                                           tttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGGCCACGATGCACtt                                                                                                                                        <  4:382554/148‑1 (MQ=255) tttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACtt                                                                                                                                        <  4:258236/148‑1 (MQ=255) tttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACtt                                                                                                                                        >  3:21095/1‑148 (MQ=255) tttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACtt                                                                                                                                        <  4:382548/148‑1 (MQ=255)  ttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTg                                                                                                                                       >  4:220668/1‑148 (MQ=255)  ttttCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTg                                                                                                                                       >  4:351563/1‑148 (MQ=255)         ataCGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCg                                                                                                                                >  3:9186/1‑148 (MQ=255)         ataCGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCg                                                                                                                                >  3:43097/1‑148 (MQ=255)            cGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCCACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAAc                                                                                                                             >  4:205894/1‑148 (MQ=255)              tAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACgg                                                                                                                           >  4:121607/1‑148 (MQ=255)              tAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACgg                                                                                                                           >  3:164766/1‑148 (MQ=255)                  acCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCa                                                                                                                       <  4:403074/148‑1 (MQ=255)                  acCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCa                                                                                                                       <  4:354463/148‑1 (MQ=255)                       ttGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGGCATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAAcc                                                                                                                  <  3:305536/148‑1 (MQ=255)                        tGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACct                                                                                                                 <  4:83685/148‑1 (MQ=255)                              tctACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGt                                                                                                           <  4:145914/148‑1 (MQ=255)                                            gAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACTCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTcac                                                                                             >  3:219698/1‑148 (MQ=255)                                            gAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTcac                                                                                             >  3:115003/1‑148 (MQ=255)                                            gAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTcac                                                                                             >  3:398978/1‑148 (MQ=255)                                            gAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATAAAATCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCCAACGGGCCAAAACCTTCTTGTCTAAATCCATTcac                                                                                             >  4:373780/1‑148 (MQ=255)                                              aTTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACAt                                                                                           >  3:253302/1‑148 (MQ=255)                                                ttCAGTTACAAAGGCACGTGTTCCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCCTCTTGTCTAAATCCAtt                                                                                                >  2:25831/1‑141 (MQ=255)                                                     ttACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGgtgt                                                                                    <  3:193694/148‑1 (MQ=255)                                                     ttACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGgtgt                                                                                    <  3:57346/148‑1 (MQ=255)                                                        cAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAg                                                                                        >  1:42411/1‑141 (MQ=255)                                                           aGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATg                                                                              <  3:373990/148‑1 (MQ=255)                                                             gCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGAt                                                                            >  4:350894/1‑148 (MQ=255)                                                                   gtTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTg                                                                      >  3:102003/1‑148 (MQ=255)                                                                          cGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAac                                                               <  4:376260/148‑1 (MQ=255)                                                                             ttAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACAcc                                                            <  4:167789/148‑1 (MQ=255)                                                                                 gTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGTCCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                        <  4:331318/148‑1 (MQ=255)                                                                                 gTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                        <  3:207818/148‑1 (MQ=255)                                                                                 gTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                        <  3:310858/148‑1 (MQ=255)                                                                                 gTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                        <  4:129160/148‑1 (MQ=255)                                                                                 gTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACAGCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                        <  4:350954/148‑1 (MQ=255)                                                                                     ttACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCaa                                                    <  4:52209/148‑1 (MQ=255)                                                                                        cGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGa                                                 <  4:9186/148‑1 (MQ=255)                                                                                        cGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGGTTTATGATAGCCTGCTTCAACACCTGCATCAAAGa                                                 <  4:43097/148‑1 (MQ=255)                                                                                          tttCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAGCCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAAt                                               <  4:391932/147‑1 (MQ=255)                                                                                          cTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAAt                                               <  4:52699/148‑1 (MQ=255)                                                                                          cTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAAt                                               <  4:239546/148‑1 (MQ=255)                                                                                          cTTCATCGCTGGATGTAAATATGCTCTTGAAGCGGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATc                                                      <  2:4283/141‑1 (MQ=255)                                                                                            tCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGa                                             <  3:155048/148‑1 (MQ=255)                                                                                             cATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCaaa                                                   <  1:46513/141‑1 (MQ=255)                                                                                                cGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTgg                                         <  3:266924/148‑1 (MQ=255)                                                                                                cGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTgg                                         <  3:342152/148‑1 (MQ=255)                                                                                                cGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTgg                                         <  3:350894/148‑1 (MQ=255)                                                                                                      aTGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATaaa                                   <  4:203392/148‑1 (MQ=255)                                                                                                      aTGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATaaa                                   <  4:258650/148‑1 (MQ=255)                                                                                                      aTGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATaaa                                   <  4:242874/148‑1 (MQ=255)                                                                                                       tGTAAATTTGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGACCGGTCCAAAACCTTCTTGTCTAAATCCCTTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTgg                                         <  2:2892/141‑1 (MQ=255)                                                                                                       tGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAg                                  <  3:304383/148‑1 (MQ=255)                                                                                                                 ctctTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGc                        <  4:21095/148‑1 (MQ=255)                                                                                                                     tGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGc                    >  3:357064/1‑148 (MQ=255)                                                                                                                              cATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGtttt           <  3:220668/148‑1 (MQ=255)                                                                                                                              cATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGtttt           <  3:351563/148‑1 (MQ=255)                                                                                                                                       aCCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTAAtt  <  3:205894/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                           TTTTTCTTATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGTACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTAATT  >  USA300TCH1516_ALE/2750419‑2750700

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑