Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,026,958	C→T	9.8%	G330D (GGT→GAT)	vraS ←	Sensor protein VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,026,958	0	C	T	9.8%	135.0 / 7.2	51	G330D (GGT→GAT)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand):  ref base C (19/27);  new base T (2/3);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.44e-01

CCAACTACTTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCTCAACAATAA  >  USA300TCH1516_ALE/2026819‑2027097                                                                                                                                            |                                                                                                                                             ctcactactTCCATATCCCTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTAcc                                                                                                                                             <  1:585383/138‑1 (MQ=255) cccagcactTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTAcc                                                                                                                                             <  1:585425/135‑1 (MQ=255)    actactTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTATCTGa                                                                                                                                          >  1:645206/1‑141 (MQ=255)     ctactTTAATGTCACTTTGCGTTGATAGATAACTTGAAATTCGTATACGGACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTTCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGaa                                                                                                                                         <  1:628038/141‑1 (MQ=255)          tCAATATCACTTTGCGTTGATAGATAACTTGAGATTCCTATACGTACCATTTCATGCTCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTCTACCTGAATCttg                                                                                                                                    >  1:198444/1‑139 (MQ=255)              tatCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAt                                                                                                                                <  1:177911/141‑1 (MQ=255)              tatCACTTTGCGTTGATAGACAACTTGAAATTCCTATACCTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAt                                                                                                                                <  1:685897/141‑1 (MQ=255)              tatCACTTGGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAt                                                                                                                                <  1:505573/141‑1 (MQ=255)                       gCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTCTTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAata                                                                                                                      >  1:633823/1‑141 (MQ=255)                         gTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATg                                                                                                                    <  1:37329/141‑1 (MQ=255)                             atagataACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGATGCTTTCACCTCGATACGTATACCTGAATCTCACAAT‑GATACGATATTGAAc                                                                                                                >  1:84266/1‑141 (MQ=255)                                      ttGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATC‑CGCACTCTGTAGAATATGGAACGTTGCACCa                                                                                                       <  1:599376/141‑1 (MQ=255)                                               cTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATGCACTATGGAACGTTTCACCAATTTCCaaa                                                                                              >  1:724949/1‑141 (MQ=255)                                                 ataCGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACATGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGc                                                                                            >  1:600675/1‑141 (MQ=255)                                                    cGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGctct                                                                                         <  1:711612/141‑1 (MQ=255)                                                           tttCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTCAATGAAGGTGCTTTCACCTCGATACGTGTACCTGAATCGCGCAAT‑GATACAAGATGGAACGTTGCACCAATTTCCAACGCTCTTTCActc                                                                                  >  1:677188/1‑139 (MQ=255)                                                              cATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTATCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCata                                                                               <  1:573083/141‑1 (MQ=255)                                                              cATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTATCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCata                                                                               <  1:221042/141‑1 (MQ=255)                                                              cATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCata                                                                               <  1:256035/141‑1 (MQ=255)                                                              cATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCata                                                                               <  1:127583/141‑1 (MQ=255)                                                                tGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATAtt                                                                             <  1:509012/141‑1 (MQ=255)                                                                         acaaacaaTACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTcc                                                                    <  1:179152/141‑1 (MQ=255)                                                                             acaaTACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATaa                                                                <  1:131924/141‑1 (MQ=255)                                                                                           gTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTATCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAAttt                                                  <  1:390982/141‑1 (MQ=255)                                                                                             cATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAGGTCCCTAACTTTGTTCTAtttttt                                                >  1:626612/1‑141 (MQ=255)                                                                                                 cGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTtcatc                                            <  1:399076/141‑1 (MQ=255)                                                                                                      cctcctTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTGTAATTTTTCGTCAACAt                                       >  1:97258/1‑141 (MQ=255)                                                                                                       ctcctTATTTAAAGGTGCTATACACTCTATGCTTGTACCAGGCTCGGGCACC‑GTGACAGTATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACAtt                                      <  1:588520/141‑1 (MQ=255)                                                                                                            tATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAAc                                 <  1:323777/141‑1 (MQ=255)                                                                                                            tATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAAc                                 <  1:566562/141‑1 (MQ=255)                                                                                                               ttAAAGGTGCTTTCACCTCGATACGTGTATCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCtt                              >  1:788978/1‑141 (MQ=255)                                                                                                                tAACGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑TATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCttt                             <  1:745113/141‑1 (MQ=255)                                                                                                                   aGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCACT‑GATACAATATGACAGGCTGCGCCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTAcc                          >  1:154642/1‑141 (MQ=255)                                                                                                                   aGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTAcc                          >  1:708027/1‑141 (MQ=255)                                                                                                                   aGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTAcc                          >  1:16319/1‑141 (MQ=255)                                                                                                                     gTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCAt                        >  1:64726/1‑141 (MQ=255)                                                                                                                        cTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTAt                     >  1:525974/1‑141 (MQ=255)                                                                                                                        cTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTAt                     >  1:325179/1‑141 (MQ=255)                                                                                                                        cTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTAt                     >  1:804162/1‑141 (MQ=255)                                                                                                                        cTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTAt                     >  1:88749/1‑141 (MQ=255)                                                                                                                         tttCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATCCAATAAGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATc                    <  1:758365/141‑1 (MQ=255)                                                                                                                         tttCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATc                    <  1:209320/141‑1 (MQ=255)                                                                                                                         tttCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATc                    <  1:28022/141‑1 (MQ=255)                                                                                                                         tttCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATc                    <  1:698621/141‑1 (MQ=255)                                                                                                                         tttCACCTCGATACGTGTACCTGAATCTGGCAAT‑GACACAATTTGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATc                    <  1:223090/141‑1 (MQ=255)                                                                                                                           tCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACCTTAAAACCTTTACCATTATCtt                  >  1:16421/1‑141 (MQ=255)                                                                                                                           tCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCtt                  >  1:14023/1‑141 (MQ=255)                                                                                                                           tCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGGTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCGTCACCTTTAGCACTTTTACCATTATCtt                  >  1:16184/1‑141 (MQ=255)                                                                                                                            cACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTg                 <  1:505783/141‑1 (MQ=255)                                                                                                                                ccGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGGCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAAtt             <  1:111561/140‑1 (MQ=255)                                                                                                                                  gATACGGGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATtct           <  1:268500/141‑1 (MQ=255)                                                                                                                                          tACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCTCAACaata   <  1:64100/141‑1 (MQ=255)                                                                                                                                           aCCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCTCAACaataa  <  1:585995/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             CCAACTACTTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAAT‑GATACAATATGGAACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCTCAACAATAA  >  USA300TCH1516_ALE/2026819‑2027097

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑