Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,454,626	A→T	L48L (CTA→CTT)	USA300HOU_2315 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,454,626	0	A	T	100.0%	122.5 / NA	38	L48L (CTA→CTT)	USA300HOU_2315	hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/25);  total (13/25)

ATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCT  >  CP000730/2454493‑2454763                                                                                                                                      |                                                                                                                                          aTAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                                    <  1:96028/141‑1 (MQ=255)  tAAAATTTCTGGTTTTCACTGGGCAATGACGATTTTCGACTTCTTTGTCATTACAATGGCGTTATCCCTTATGCCCAGCGACTTACAGTCGTGGAGGGGTGTCAAACACTTTATATTTGGAGTTACCGATCTTGCTCCAtt                                                                                                                                   >  1:174936/1‑141 (MQ=255)        ttCTGGTTTTCAATGGGCAATGACGAGTTTCGTCTTCTTTGTCATTACCATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTGACAGATCTTGCACCATTAATtgc                                                                                                                             <  1:450272/141‑1 (MQ=255)                          attgtcgagtatcgtcgTCTTTCTTATTACAATGGCGTTATCCCATAAATTCGCATATTTCCAGTCTATAAGTGGTGTCAAACACTTTATATTTTAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACt                                                                                                           <  1:580560/130‑1 (MQ=255)                          aaTGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATACTGCACCATTAATTGCTGCAATCATTTGTATACt                                                                                                           <  1:919036/141‑1 (MQ=255)                                   tttCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCaa                                                                                                  <  1:491712/141‑1 (MQ=255)                                       gTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAatat                                                                                              >  1:414791/1‑141 (MQ=255)                                           tcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaaaa                                                                                          <  1:371883/141‑1 (MQ=255)                                                 tCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTcc                                                                                    <  1:834528/141‑1 (MQ=255)                                                 tCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTcc                                                                                    >  1:730668/1‑141 (MQ=255)                                                     tACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACt                                                                                <  1:530722/141‑1 (MQ=255)                                                            gCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGt                                                                         >  1:782669/1‑141 (MQ=255)                                                            gCGTTATCCATTATGCTCAGAGATTTCCAGGCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGt                                                                         <  1:614/141‑1 (MQ=255)                                                                     aTTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATtc                                                                >  1:661154/1‑141 (MQ=255)                                                                         tGCTCAGAGATTTCCAGTCTATAATTCGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCaa                                                            <  1:563545/141‑1 (MQ=255)                                                                           cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                          <  1:517212/141‑1 (MQ=255)                                                                           cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                          <  1:154125/141‑1 (MQ=255)                                                                           cTCAGAGATTTCCAGGCTATAATTGGAGTCAAACCCATTACAGTTGAAGTTACAGATCTTGCACCATGAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                          <  1:22323/141‑1 (MQ=255)                                                                            tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                                         <  1:138677/141‑1 (MQ=255)                                                                            tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                                         <  1:738823/141‑1 (MQ=255)                                                                                  aTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTTCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGa                                                   >  1:872780/1‑141 (MQ=255)                                                                                        aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                             <  1:94239/141‑1 (MQ=255)                                                                                               aaTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACg                                      <  1:672586/141‑1 (MQ=255)                                                                                                    gtgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAGCGTCTAt                                 <  1:447242/141‑1 (MQ=255)                                                                                                      gtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTg                               <  1:661839/141‑1 (MQ=255)                                                                                                            cacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                         <  1:526340/141‑1 (MQ=255)                                                                                                             acTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCtt                        <  1:354781/141‑1 (MQ=255)                                                                                                               tttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAACGTAATTGAACGTATATTGCTGGCTTTa                      >  1:886942/1‑141 (MQ=255)                                                                                                               tttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTa                      >  1:14703/1‑141 (MQ=255)                                                                                                                  atatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAACATTCTCAATCAGCCGGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtt                   >  1:865458/1‑141 (MQ=255)                                                                                                                  atatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtt                   >  1:147047/1‑141 (MQ=255)                                                                                                                    atTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtttt                 <  1:589851/141‑1 (MQ=255)                                                                                                                        gAAGTTACAGATCTTGCACCAGTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAGTTTACCt             >  1:134211/1‑141 (MQ=255)                                                                                                                          aGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCttt           <  1:835733/141‑1 (MQ=255)                                                                                                                          aGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCttt           <  1:926938/141‑1 (MQ=255)                                                                                                                              aCAGATCTTGCACCACTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatt       >  1:687541/1‑141 (MQ=255)                                                                                                                                 gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAACAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattatt    >  1:584648/1‑141 (MQ=255)                                                                                                                                   tCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCt  <  1:413702/141‑1 (MQ=255)                                                                                                                                      |                                                                                                                                          ATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCT  >  CP000730/2454493‑2454763

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: ‑