Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	531,823	A→G	13.4%	M75V (ATG→GTG)	purR →	Pur operon repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	531,823	0	A	G	13.4%	62.0 / 5.3	30	M75V (ATG→GTG)	purR	Pur operon repressor
Reads supporting (aligned to +/- strand):  ref base A (13/13);  new base G (2/2);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.16e-02

GAAAAAATTTAAACAGGCGAAGTCTTCAATAAGTGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGCTACTAAACAAAGTTGGT  >  USA300TCH1516_ALE/531690‑531957                                                                                                                                      |                                                                                                                                       gAAAAAATTTAAACAGGCGAAGTCTTCAATAAGTGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTaa                                                                                                                                 >  1:220830/1‑141 (MQ=255)                              aaaGTGATGATTTCCAAATTAGAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAgg                                                                                                    <  2:249573/140‑1 (MQ=255)                              aaaGTGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAATTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAgg                                                                                                    <  2:249654/140‑1 (MQ=255)                                 gTGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCa                                                                                                 >  2:11677/1‑141 (MQ=255)                                 atGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCa                                                                                                 <  1:256135/140‑1 (MQ=255)                                  tGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCAt                                                                                                >  1:308295/1‑141 (MQ=255)                                             aaaTTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTag                                                                                     >  2:300072/1‑141 (MQ=255)                                                   taAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAACCCAATGATGAGTAAAGAAGCGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAtaga                                                                               <  2:289051/141‑1 (MQ=255)                                                   taAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAgaga                                                                               >  1:54131/1‑141 (MQ=255)                                                     aaaaaTACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGGTGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGagaaa                                                                             >  1:272717/1‑141 (MQ=255)                                                     aaaaaTACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGGTGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGagaaa                                                                             >  1:272687/1‑141 (MQ=255)                                                     aaaaaTACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGATGTCATTACTCTATTAGAAGagaaa                                                                             <  1:251639/141‑1 (MQ=255)                                                                       gaaaagTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTggg                                                           >  2:309044/1‑140 (MQ=255)                                                                           agTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGGTGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGat                                                       <  2:272717/141‑1 (MQ=255)                                                                           agTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGGTGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGat                                                       <  2:272687/141‑1 (MQ=255)                                                                                           tactacTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGa                                       >  1:268133/1‑141 (MQ=255)                                                                                               actGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTg                                   >  1:259113/1‑141 (MQ=255)                                                                                                    tgGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGGAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTTCCTGGCGGATATTTATTTTTATCAGATTTggtagg                              >  2:24551/1‑141 (MQ=255)                                                                                                     ggCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTggtaggt                             <  1:19716/141‑1 (MQ=255)                                                                                                      gcgcAAGTGGTGGTGTTACGTATAAACCAATGATCAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTggtaggta                            <  2:328712/141‑1 (MQ=255)                                                                                                        gcAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGACCGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAAt                          <  1:11677/141‑1 (MQ=255)                                                                                                         cAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATc                         <  1:281975/141‑1 (MQ=255)                                                                                                           aggggtggtgTTACGTAAAAACTAAAGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCa                       <  1:281769/138‑1 (MQ=255)                                                                                                               gtggtgTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACATGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGc                   >  1:280098/1‑141 (MQ=255)                                                                                                                  gtgtTACGTAGAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGctac                <  2:269976/141‑1 (MQ=255)                                                                                                                   tgtTACGTAAAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGctact               <  1:114443/141‑1 (MQ=255)                                                                                                                     ttACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATTCATCGCTACTaa             <  1:243763/141‑1 (MQ=255)                                                                                                                        cttagaaaCCAAGGATGAGTAAAAAAGAGGCGACTGAAGTTGTTAATGAGTTCATTACTCAATTAAAAGAGAAAGAACGTTTGTTACCTAGCGCATATTTATGTTTATCTTATTTGGTAGGTCATCCATCGCGACTAAACa          >  2:89178/6‑141 (MQ=255)                                                                                                                            taAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGCTACTAAACAAAGt      >  2:94651/1‑141 (MQ=255)                                                                                                                                ccAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGCTACTAAACAAAGTTGGt  >  1:282048/1‑141 (MQ=255)                                                                                                                                      |                                                                                                                                       GAAAAAATTTAAACAGGCGAAGTCTTCAATAAGTGAAGATGTCCAAATTATAAAAAATACATTCCAAAAAGAAAAGTTAGGTACAGTAATTACTACTGCTGGCGCAAGTGGTGGTGTTACGTATAAACCAATGATGAGTAAAGAAGAGGCGACTGAAGTTGTTAATGAGGTCATTACTCTATTAGAAGAGAAAGAACGTTTGTTACCTGGCGGATATTTATTTTTATCAGATTTGGTAGGTAATCCATCGCTACTAAACAAAGTTGGT  >  USA300TCH1516_ALE/531690‑531957

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: ‑