Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,299,770	T→A	9.5%	P477P (CCT→CCA)	rnjB →	beta‑lactamase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,299,770	0	T	A	9.5%	127.7 / 5.0	42	P477P (CCT→CCA)	rnjB	beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base T (18/20);  new base A (2/2);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

ATGATATTAAATGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAGAAAAACGCAT  >  CP000730/1299630‑1299907                                                                                                                                             |                                                                                                                                          atgatatTAAATGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCt                                                                                                                                           <  1:431487/141‑1 (MQ=255)        tAAATGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATa                                                                                                                                    <  2:203498/141‑1 (MQ=255)           aTGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGAc                                                                                                                                 >  1:126328/1‑141 (MQ=255)            tGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACg                                                                                                                                <  2:524697/141‑1 (MQ=255)              aaaaGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGta                                                                                                                              >  2:778541/1‑141 (MQ=255)               aaaGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGtat                                                                                                                             >  1:253191/1‑141 (MQ=255)                aaGGTAAATTCAGGACATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGtata                                                                                                                            <  1:654465/141‑1 (MQ=255)                     aaaTTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGc                                                                                                                       <  2:473717/141‑1 (MQ=255)                        ttCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCggg                                                                                                                    >  2:446174/1‑141 (MQ=255)                         tCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGa                                                                                                                   <  2:724263/141‑1 (MQ=255)                          cAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGAc                                                                                                                  <  1:961/141‑1 (MQ=255)                                acatctagaTAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGaaa                                                                                                            <  2:424642/133‑1 (MQ=255)                                 tatTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAAt                                                                                                           <  2:57893/141‑1 (MQ=255)                                 tatTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCAAAAAATAGACGTATAGCTGCGGGACCTGAAAt                                                                                                           >  1:736365/1‑141 (MQ=255)                                 tatTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCAAAAAATAGACGTATAGCTGCGGGACCTGAAAt                                                                                                           >  1:736356/1‑141 (MQ=255)                                        aTAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAAtct                                                                                                    <  2:85670/141‑1 (MQ=255)                                            aTGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTg                                                                                                <  2:148270/141‑1 (MQ=255)                                                     gTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGCTAATATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGtat                                                                                       >  1:214015/1‑141 (MQ=255)                                                            ggATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACg                                                                                <  1:101477/141‑1 (MQ=255)                                                              aTGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAACTAGACGTATAGCTGCGGGACCTGAAATTCCATCTCGTTGGCTAGTATATGTACGTg                                                                              >  2:622905/1‑141 (MQ=255)                                                               tGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCGATCTCGTGGGTTTGTATATGTACGTGa                                                                             <  2:549458/141‑1 (MQ=255)                                                                            gtgtTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACtta                                                                <  1:710750/141‑1 (MQ=255)                                                                            gtgtTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACtta                                                                >  2:520723/1‑141 (MQ=255)                                                                             tgtTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACttat                                                               >  1:286719/1‑141 (MQ=255)                                                                              gtTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACttatt                                                              <  1:775408/141‑1 (MQ=255)                                                                               ttGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAACAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACttatta                                                             >  2:686086/1‑141 (MQ=255)                                                                                            aTCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCagaag                                                >  1:143930/1‑141 (MQ=255)                                                                                                 ttAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCGCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGaaa                                           >  1:446068/1‑141 (MQ=255)                                                                                                  tAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAg                                          <  2:348645/141‑1 (MQ=255)                                                                                                       gaagaTGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCCGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGt                                     <  2:680940/141‑1 (MQ=255)                                                                                                        aagaTGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTg                                    >  1:84832/1‑141 (MQ=255)                                                                                                        aagaTGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTg                                    >  1:216040/1‑141 (MQ=255)                                                                                                         agaTGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGa                                   >  2:141125/1‑141 (MQ=255)                                                                                                              gTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAAtag                              <  1:236397/141‑1 (MQ=255)                                                                                                                     tATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGc                       <  2:53296/141‑1 (MQ=255)                                                                                                                        tGCTGTTGTAACGTTAGATCCAAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTgg                    <  2:736365/141‑1 (MQ=255)                                                                                                                        tGCTGTTGTAACGTTAGATCCAAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTgg                    <  2:736356/141‑1 (MQ=255)                                                                                                                         gCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGt                   >  2:269901/1‑141 (MQ=255)                                                                                                                          cTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGtt                  >  1:341936/1‑141 (MQ=255)                                                                                                                                tAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAg            >  2:307375/1‑141 (MQ=255)                                                                                                                                  aCGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAGaa          >  2:370029/1‑141 (MQ=255)                                                                                                                                          tCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAGAAAAACGCAt  <  1:520723/141‑1 (MQ=255)                                                                                                                                          tCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAGAAAAACGCAt  <  2:341936/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                          ATGATATTAAATGAAAAGGTAAATTCAGGAAATATTTTAATAGATGGCATTGGTATTGGGGATGTAGGAAATATCGTGTTGAGAGACCGTCATCTTTTAGCAGAAGATGGTATCTTTATTGCTGTTGTAACGTTAGATCCTAAAAATAGACGTATAGCTGCGGGACCTGAAATTCAATCTCGTGGGTTTGTATATGTACGTGAAAGTGAAGACTTATTACGTGAAGCAGAAGAGAAAGTACGTGAAATAGTAGAGGCTGGTTTACAAGAAAAACGCAT  >  CP000730/1299630‑1299907

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑