Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,343,016	A→G	10.5%	T40A (ACT→GCT)	USA300HOU_2200 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,343,016	0	A	G	10.5%	93.0 / 4.1	38	T40A (ACT→GCT)	USA300HOU_2200	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (15/19);  new base G (2/2);  total (17/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

AACCCGAAAAGGAGATTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACAGTAAAGTAAAAAATGAATTAGC  >  CP000730/2342877‑2343155                                                                                                                                            |                                                                                                                                            aatccGTAAAGGAGAGTGTGGGATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGAc                                                                                                                                            >  2:90986/4‑141 (MQ=255)       aaaaGGAGATTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGa                                                                                                                                      >  1:285528/1‑141 (MQ=255)             agaTTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGGCTGTGGATGGTTa                                                                                                                                >  2:151241/1‑141 (MQ=255)             agaTTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGGCTGTGGATGGTTa                                                                                                                                >  2:151202/1‑141 (MQ=255)              gagtGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTCGCATTGGGATTATTATCACAGGTCGGCGCTGCATTAAAGAGTCACGAAGCAGCTGCAGATAGTAATAACGGCTATAAAGAAAGGACTGTGGATGGTTAt                                                                                                                               >  2:8396/4‑141 (MQ=255)              gaTTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTAGTATCAATGGTCGGTTCTTCATTTCCTAGTCACGAAGCATCTTCAGATAGTAATAACGGCTAGAAAGAAATGACTGTGGATTGTTAt                                                                                                                               >  1:340773/1‑141 (MQ=255)                ttGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATca                                                                                                                             <  1:434344/141‑1 (MQ=255)                  gagaTATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATcaca                                                                                                                           >  2:173071/1‑141 (MQ=255)                  gagaTATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATcaca                                                                                                                           <  2:222355/141‑1 (MQ=255)                   agaTATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCacac                                                                                                                          <  1:164006/141‑1 (MQ=255)                   agaTACGAACCTACACTCATTTACAACCGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTACATTACCGAGCCACGAAACATCTGCAGATAGTAATAACGGCTATAACGACATGACTGTGGATGGTTATCacac                                                                                                                          <  2:269570/141‑1 (MQ=255)                                  aTCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAAt                                                                                                           >  2:51522/1‑141 (MQ=255)                                       ttGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAg                                                                                                      <  1:164336/141‑1 (MQ=255)                                                ccACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTa                                                                                             <  1:85556/141‑1 (MQ=255)                                                   cTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGGCTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTa                                                                                          <  1:151202/141‑1 (MQ=255)                                                   cTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGGCTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTa                                                                                          <  1:151241/141‑1 (MQ=255)                                                   cTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTa                                                                                          >  2:190383/1‑141 (MQ=255)                                                    tttAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTAc                                                                                         <  2:128865/141‑1 (MQ=255)                                                         cATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTGTTACTGCAt                                                                                    >  2:162170/1‑141 (MQ=255)                                                         cATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCAt                                                                                    <  1:125055/141‑1 (MQ=255)                                                                      atCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAactta                                                                       >  1:442757/1‑141 (MQ=255)                                                                               cGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCtt                                                              >  1:363836/1‑141 (MQ=255)                                                                                  aGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTccc                                                           >  2:302962/1‑141 (MQ=255)                                                                                     tGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGa                                                        <  1:172158/141‑1 (MQ=255)                                                                                     tGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGa                                                        >  1:245708/1‑141 (MQ=255)                                                                                         ttACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAAt                                                    <  2:285528/141‑1 (MQ=255)                                                                                             cGAGTCACGAAGCATCTGCAGAGAGTGGTTACTGCAATAAATAAACTACTAGGTGTTTGTATCACACGGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATaaaa                                                <  1:268141/141‑1 (MQ=255)                                                                                                  cACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGtt                                           <  2:36893/141‑1 (MQ=255)                                                                                                         cATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATc                                    <  2:190228/141‑1 (MQ=255)                                                                                                          aTCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCa                                   <  1:443736/141‑1 (MQ=255)                                                                                                            cTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAg                                 <  1:23437/141‑1 (MQ=255)                                                                                                                 gATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAAtt                            <  1:406610/141‑1 (MQ=255)                                                                                                                 gATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAAtt                            <  1:406615/141‑1 (MQ=255)                                                                                                                        ataaCGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACagta                     >  1:66887/1‑141 (MQ=255)                                                                                                                            cGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTACTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACagtaaaat                 <  2:408202/141‑3 (MQ=255)                                                                                                                                 ataAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACAGTAAAGTaaaaa            >  2:148690/1‑141 (MQ=255)                                                                                                                                          tGACTGTGGATGGTTATCACACTGTTCCTTACACAATGTCAGTAGATTGTATTACTGCATTACATCGAACTTACTTTATCATCCCAGAAAATAAAAATGTTCTTTATTAAGAAATTGACAGTAAAGTAAAAaattaattcg   <  2:375859/141‑3 (MQ=255)                                                                                                                                           gACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACAGTAAAGTAAAAAATGAATTAGc  >  2:108171/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            AACCCGAAAAGGAGATTGAGATATGAAACTAAAATCATTTGTTACTGCCACTTTAGCATTGGGATTATTATCAACGGTCGGAGCTGCATTACCGAGTCACGAAGCATCTGCAGATAGTAATAACGGCTATAAAGAAATGACTGTGGATGGTTATCACACTGTTCCTTACACAATTTCAGTAGATGGTATTACTGCATTACATCGAACTTACTTTATCTTCCCAGAAAATAAAAATGTTCTTTATCAAGAAATTGACAGTAAAGTAAAAAATGAATTAGC  >  CP000730/2342877‑2343155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑