Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	267,872	T→C	13.0%	R525R (CGT→CGC)	USA300HOU_0238 →	staphylocoagulase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	267,872	0	T	C	13.0%	80.1 / 2.5	39	R525R (CGT→CGC)	USA300HOU_0238	staphylocoagulase
Reads supporting (aligned to +/- strand):  ref base T (21/12);  new base C (3/2);  total (25/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

GTACAGGTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATACAACGTAACAACACATGCAAACGG  >  CP000730/267742‑268012                                                                                                                                    |                                                                                                                                             gTACAGGTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACaaa                                                                                                                                    <  2:353139/141‑1 (MQ=255)  tACAGGTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAAAGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACaaaa                                                                                                                                   >  1:409413/1‑141 (MQ=255)   gcAGGTATCCGTGAATACAACGAGATAACATTTGGATAAAAAGCGAGACCAAGACGCAATAATCCTTCAGAAACAAATGCATATAACATAAAAACACATGC‑AAATGGGCAAATATCATATAGAACTCAACCTACaaaaaaa                                                                                                                                  >  2:33080/2‑140 (MQ=255)   aCAGGTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAAc                                                                                                                                  >  2:83518/1‑141 (MQ=255)      ggTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAAcaag                                                                                                                               >  1:148991/1‑141 (MQ=255)          tCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAAcaagccaa                                                                                                                           >  2:212433/1‑141 (MQ=255)              tGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCaa                                                                                                                       <  2:184238/141‑1 (MQ=255)                  tACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAaaaca                                                                                                                   >  1:54412/1‑141 (MQ=255)                                     gATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGCAAAATGGTCAAGTAACATACGGAGCTCGCCCAACACACAACAAGCCAAGCAAAACAAACGCATACAACGTaaaa                                                                                                 >  2:239065/1‑139 (MQ=21)                                      atatGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTaacaac                                                                                               >  1:126291/1‑141 (MQ=255)                                               gagaCCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGaaa                                                                                      >  1:5277/1‑141 (MQ=255)                                                agaCCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAAc                                                                                     >  1:144486/1‑141 (MQ=255)                                                       gATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAg                                                                              <  1:329342/141‑1 (MQ=255)                                                       gATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGCAAACGGCCAAg                                                                              >  2:99615/1‑141 (MQ=255)                                                          tCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTAt                                                                           <  1:274601/141‑1 (MQ=255)                                                             aTAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATACAACGTAACAACACATGCAAACGGCCAAGTATCaa                                                                        >  2:84400/1‑140 (MQ=255)                                                              tAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGTTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCata                                                                       <  2:274857/141‑1 (MQ=255)                                                                  ccATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGCAAACGGCCAAGTATCATATggg                                                                   >  2:307318/1‑140 (MQ=255)                                                                    aTCAGAAACAAATGCATATAACGTAACTACTTATTC‑ATGTTGCGAAGAACCATGCGGTCCTCGCCCGACGCAAAACAAGCCCAGTACACGAAACTCATACAACGTAACTACCCCCAAAGACGGCCAATTATCATATGgctc                                                                 <  2:342298/141‑3 (MQ=255)                                                                     tCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTAACATATGGCGCt                                                                >  2:275268/1‑141 (MQ=255)                                                                       aGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATACAACGTAACAACACATGGAAACGGCCAAGTAACATATAGCGCACg                                                              >  2:14700/1‑141 (MQ=255)                                                                            cAAATGCATACAACGTAACAACACATGC‑AAATGGTCAAGTATCATATGGCGCTCGCCCGACACAAAAAAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGCAGATGGTAACGTAACATACGGAGCTCGcgaaa                                                         >  2:223452/1‑137 (MQ=11)                                                                             aaaTGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAac                                                        <  1:202379/141‑1 (MQ=255)                                                                              aaTGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAaca                                                       >  1:404538/1‑141 (MQ=255)                                                                               aTGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAacac                                                      >  1:130313/1‑141 (MQ=255)                                                                                 gCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACaa                                                    >  1:97208/1‑141 (MQ=255)                                                                                        aCGTAACAACACATGC‑AAATGGTCAAGTATCATACGGTGCTCGCCCAACACAAAAAAAGCCAAGCAAAACAAATGCATACAACGTAACAACACATGCAAATGGTCAAGTATCATATGGCGCTCGCCCGACACAAAAaaagc                                             <  1:277876/141‑1 (MQ=11)                                                                                        aCGTAACAACACATGC‑AAATGATTAAGTATCATACGGTGCTAGCATAAAAAAAAAAAAGTAAAGCGAAATAAATGAATAAAACGTAAAAATACATGAAAATGGTAAGGTGTCATATGGCGATAGAAAAACAAAAAAaaagc                                             >  2:106448/1‑141 (MQ=255)                                                                                            aacaacACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAAcaagccaag                                         <  1:40253/141‑1 (MQ=255)                                                                                             acgacacATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGACCAAGTATCATATGGCGCTCGCCCAACACAAAAcaagccaagc                                        <  2:177808/138‑1 (MQ=255)                                                                                               aacaCATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCaa                                      <  1:117106/141‑1 (MQ=255)                                                                                               aacaCATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCaa                                      <  1:76772/141‑1 (MQ=255)                                                                                                         aaaTGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGc                             >  2:274627/1‑141 (MQ=255)                                                                                                            tGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGGTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATa                          >  1:386996/1‑141 (MQ=255)                                                                                                            tGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATa                          >  2:327702/1‑141 (MQ=255)                                                                                                            tGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATa                          <  1:127792/141‑1 (MQ=255)                                                                                                            tGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGACGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATa                          >  2:292618/1‑141 (MQ=255)                                                                                                                          aCGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATACAACGTAACAacac            <  2:48746/141‑1 (MQ=255)                                                                                                                               gCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATACAACGTAACAACACATGCa       >  2:271555/1‑141 (MQ=255)                                                                                                                                    tCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATACAACGTAACAACACATGCAAACgg  >  1:69574/1‑141 (MQ=255)                                                                                                                                    |                                                                                                                                             GTACAGGTATCCGTGAATACAACGATGGAACATTTGGATATGAAGCGAGACCAAGATTCAATAAGCCATCAGAAACAAATGCATATAACGTAACAACACATGC‑AAATGGTCAAGTATCATACGGAGCTCGTCCGACACAAAACAAGCCAAGCAAAACAAACGCATATAACGTAACAACACATGGAAACGGCCAAGTATCATATGGCGCTCGCCCAACACAAAACAAGCCAAGCAAAACAAATGCATACAACGTAACAACACATGCAAACGG  >  CP000730/267742‑268012

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: ‑