Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	111,560	T→C	22.0%	R210R (CGT→CGC)	USA300HOU_0110 →	possible staphylococcal tandem lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	111,560	0	T	C	22.0%	89.2 / 19.7	50	R210R (CGT→CGC)	USA300HOU_0110	possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (20/17);  new base C (7/3);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

TTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTT  >  CP000730/111420‑111695                                                                                                                                             |                                                                                                                                        tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                                                                         <  1:472603/141‑1 (MQ=255)        tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAGGCAAAAGat                                                                                                                                  >  1:83205/1‑141 (MQ=255)           ttGCGGAATATAGCAATTTTAGAGATTGAATGAATTATAAAGATGGAGACATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACATTTACGCAAAAGATATg                                                                                                                               <  2:231966/141‑1 (MQ=14)           ttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATg                                                                                                                               >  2:452935/1‑141 (MQ=255)           ttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATAATTATAATGTAAAACAATTACGCAAAAGATATg                                                                                                                               >  2:319534/1‑141 (MQ=255)            tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                                                              >  2:125191/1‑141 (MQ=255)              cgcAAGATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACa                                                                                                                            <  2:446994/141‑1 (MQ=255)                cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATGTCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATCTAAATTAACTAATGAGGATTATCATGTAAGACAATTAGGTAAAGGATATGACATa                                                                                                                          >  1:56902/1‑141 (MQ=18)                 aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTGAAACAATTACGCAAAAGATATGATATAc                                                                                                                         <  2:54066/141‑1 (MQ=14)                   tataGCAATTTTAAAGATTTAATGAATTATAAGGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                                                                       >  1:409693/1‑140 (MQ=14)                   tataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                                                                       <  2:60891/141‑2 (MQ=14)                    ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                                                                      <  2:194443/141‑1 (MQ=255)                    ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                                                                      <  1:202326/141‑1 (MQ=255)                       gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                   <  2:384034/141‑1 (MQ=255)                         aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAt                                                                                                                 >  1:426072/1‑141 (MQ=255)                          aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgagta                                                                                                                >  1:552115/1‑136 (MQ=11)                          aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcaacgagta                                                                                                                >  2:275915/1‑136 (MQ=11)                               aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                                                           >  1:127623/1‑141 (MQ=255)                               aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                                                           >  1:460918/1‑141 (MQ=255)                                   aTTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                                                                       <  2:530419/141‑1 (MQ=255)                                        aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                                                                  >  1:471151/1‑141 (MQ=255)                                                taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                                                                          >  2:493352/1‑141 (MQ=255)                                                  aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                                                                        <  2:306071/141‑1 (MQ=255)                                                           aaagatCCTATAATCCAGAGGTGCCGAGTTATGCAGCTTAATATCCATTAACTAATGATGATTATAATGTAAAACCATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                               <  2:95246/137‑1 (MQ=14)                                                            tatatCATAGAATCCAGAGGTGCCGAGTTATTCAGGTCAATATCAAGTAACTAATGATGATTATAATGTAAAACAATTACGACAAAGATATGACATACCAACAAAGAAAGCGCCACAGCTGTTGTTGAAGGGTGAAGGGaa                                                                              >  2:156864/1‑141 (MQ=14)                                                               atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                                                           <  1:157110/141‑1 (MQ=255)                                                               atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                                                           <  2:299612/141‑1 (MQ=255)                                                                 cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                                                         >  2:245530/1‑141 (MQ=255)                                                                 cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                                                         >  2:245504/1‑141 (MQ=255)                                                                 cATATAATCCAGAGGGGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                                                         <  1:5479/141‑1 (MQ=255)                                                                  atagAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAAAAAGCGACGAAGCAGTTGTGAAAAGGAACAGGGAATTTaaa                                                                        >  2:222722/1‑141 (MQ=17)                                                                         ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                                                                 <  1:529958/141‑1 (MQ=255)                                                                             agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGAAAAACAATTCCGTAACAGATATGACATACCAACAAATAAAGCGCCGCAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatccg                                                             >  2:112799/1‑139 (MQ=255)                                                                               gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTAGAATGTAAAACAATTACGTAACAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGTAATTTAAAAGGTtcatccgcg                                                           >  2:285815/1‑137 (MQ=255)                                                                                             aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt                                             <  1:190504/141‑1 (MQ=255)                                                                                             aGCTCAAAATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt                                             <  1:77527/141‑1 (MQ=255)                                                                                                   atatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATCAAAATATTGGAtt                                       >  1:95495/1‑141 (MQ=255)                                                                                                     atCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTa                                     >  1:230992/1‑141 (MQ=255)                                                                                                      tCAATTAACTAATGAGGATTATAATGTAAAACAATTACGTAAAAGTTATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTAc                                    <  2:138691/141‑1 (MQ=255)                                                                                                         aTTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACttt                                 >  2:266500/1‑141 (MQ=255)                                                                                                               tAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTaga                           <  2:492576/141‑1 (MQ=255)                                                                                                                   gatgatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAAt                       >  1:48489/1‑141 (MQ=255)                                                                                                                   gatgatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAAt                       >  2:555335/1‑141 (MQ=255)                                                                                                                      gatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaaa                    >  2:422506/1‑141 (MQ=255)                                                                                                                           taATGTAAAACAAATACGAAAAAGATACGACATAGCAACAAAAAAAGCGCCGAAGCAGTTGCCGAAAAGTACATGGAATTTAAAAGTTTCATCAAAAAAAAAAAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGa               <  2:426072/141‑1 (MQ=255)                                                                                                                              tacaaaaCAATTACGAAAAAGATAAGACATACCAACAAATAAAGCGCAGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTAATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaaaa            <  2:56902/138‑1 (MQ=18)                                                                                                                                 aaaaCAATTACGTAAAGGAAATGACATACCAACAAATACAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAatat         >  1:318858/1‑141 (MQ=255)                                                                                                                                       aTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttactt   <  1:103361/141‑1 (MQ=255)                                                                                                                                       aTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttactt   >  2:140593/1‑141 (MQ=255)                                                                                                                                       aTTACGTAAAAGATAAGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttactt   >  1:422476/1‑141 (MQ=255)                                                                                                                                        ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt  <  1:196248/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                        TTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTT  >  CP000730/111420‑111695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑