Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,324,487	G→A	10.0%	R420H (CGT→CAT)	mutL →	DNA mismatch repair protein MutL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,324,487	0	G	A	10.0%	147.4 / 5.1	54	R420H (CGT→CAT)	mutL	DNA mismatch repair protein MutL
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (2/4);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 6.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.44e-01

AGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGATATT  >  USA300TCH1516_ALE/1324347‑1324626                                                                                                                                              |                                                                                                                                            agaaAGTAAGAATACGCCATTGATTGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACg                                                                                                                                             <  2:329493/141‑1 (MQ=255)  gaaAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATGAGGTAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGt                                                                                                                                            <  2:94880/141‑1 (MQ=255)        aaCAGTAAGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGaaaaa                                                                                                                                      >  1:281555/1‑141 (MQ=255)        aaCAGCAAGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGaaaaa                                                                                                                                      <  1:216893/141‑1 (MQ=255)               aGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAg                                                                                                                               >  1:16362/1‑141 (MQ=255)               aGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTAGTTATAATAATACACGTGAACAAGATGAAg                                                                                                                               >  2:269457/1‑141 (MQ=255)                    tttATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGactac                                                                                                                          <  1:120446/141‑1 (MQ=255)                    tgtATGGAAGAAAATAAAAAAGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATAAAAAAAAAAAAGATGAAGactac                                                                                                                          <  2:142530/139‑1 (MQ=255)                       aTGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTc                                                                                                                       <  2:68933/141‑1 (MQ=255)                         ggAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAACCGTCTTAAAATTT‑ATAGAAGGAGTTGGAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCaa                                                                                                                     >  2:400425/1‑141 (MQ=255)                              aaaaTCAAAACGATGAGATAGTAATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAaac                                                                                                                <  2:340391/141‑1 (MQ=255)                                   cgcaaCGAAGAGAAAGTTATAAAAGAAGATCCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAAcaacaa                                                                                                           <  1:334647/138‑1 (MQ=255)                                      aaCGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGaa                                                                                                        >  1:118634/1‑141 (MQ=255)                                       aCGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGaaa                                                                                                       <  2:16362/141‑1 (MQ=255)                                         gATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAAtt                                                                                                     >  1:372539/1‑141 (MQ=255)                                             agatagatATAAAAGAAGATTCATATAATCCATTCGTAACGAAAATATCTAAAAGGTTAATAGCCAATAAT‑AAAACGTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTAc                                                                                                 <  2:4113/141‑1 (MQ=255)                                             agaTAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCCAAATACAACAAGAACTTTTAc                                                                                                 >  2:122011/1‑141 (MQ=255)                                               aTAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGATTATAATAATACACGTGAAAAAGATAAAGACTACTTCAAAAAACAACAAGAAATTTTACaa                                                                                               >  2:85370/1‑141 (MQ=255)                                                      taAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATgg                                                                                        <  1:270096/141‑1 (MQ=255)                                                          agaagaTTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCa                                                                                    <  1:89416/141‑1 (MQ=255)                                                              gaTTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACa                                                                                >  1:157277/1‑141 (MQ=255)                                                                ttCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATTGTACAGTAG‑TAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACAtt                                                                              <  2:398337/141‑1 (MQ=255)                                                                   atatAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGa                                                                           <  1:130403/141‑1 (MQ=255)                                                                   atatAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAAGCTTCTCGTTTTATGTACTTAGGGGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGa                                                                           <  1:194286/141‑1 (MQ=255)                                                                     ataATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACATGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGAtt                                                                         >  2:265726/1‑141 (MQ=255)                                                                     ataATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACATGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGAtt                                                                         >  2:265785/1‑141 (MQ=255)                                                                              tCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGTATCAAACATTTGATTAAAatgatg                                                                >  1:398119/1‑141 (MQ=255)                                                                               cGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATgg                                                               >  2:143018/1‑141 (MQ=255)                                                                                     gAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAAc                                                         <  2:223927/141‑1 (MQ=255)                                                                                          cATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGc                                                    >  1:327757/1‑141 (MQ=255)                                                                                          cATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGc                                                    >  1:327663/1‑141 (MQ=255)                                                                                          cATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGc                                                    >  1:174879/1‑141 (MQ=255)                                                                                          cATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATCGTACAACTGTGc                                                    >  2:288096/1‑141 (MQ=255)                                                                                           aTCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCa                                                   <  1:373385/141‑1 (MQ=255)                                                                                             ttGAAAGTTTAATAGATGATGAT‑GAATCTTCAGATTATAATAATACACGTGAAAAAGATAAATACTACTTCAAAAAACAACTATAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCaaa                                                 <  2:333961/140‑1 (MQ=255)                                                                                                       aaTAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGaa                                       >  2:379543/1‑141 (MQ=255)                                                                                                       aaTAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGaa                                       <  2:281555/141‑1 (MQ=255)                                                                                                             agatgat‑gaATCTTCTGATTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGc                                 <  2:385158/140‑1 (MQ=255)                                                                                                             agatgat‑gaAACGTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGc                                 <  2:237834/140‑1 (MQ=255)                                                                                                              gatgat‑gaATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCg                                <  1:385378/141‑1 (MQ=255)                                                                                                              gatgat‑gaATCTTCTGGTTATAATAATACACATGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCg                                <  1:265726/141‑1 (MQ=255)                                                                                                              gatgat‑gaATCTTCTGGTTATAATAATACACATGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCg                                <  1:265785/141‑1 (MQ=255)                                                                                                                     gaATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCggat                          >  1:119119/1‑141 (MQ=255)                                                                                                                       aTCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCtgatga                        >  2:208739/1‑141 (MQ=255)                                                                                                                              ggTTATAAAAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAATAAATTTTACAAGAAATGGATCAGATATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATtattat                 <  2:313035/141‑1 (MQ=255)                                                                                                                                ttATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGCCAAACCTTCTGCGCACAAATCTGCTGATGATTATTatga               <  1:391969/141‑1 (MQ=255)                                                                                                                                ttATAATAATACACGTGAAAAAGATAAAGACTACATCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTGGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTatga               <  2:302221/141‑1 (MQ=255)                                                                                                                                atataATAATACACATGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTatga               <  2:394934/140‑1 (MQ=255)                                                                                                                                   taataataCACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGt            >  2:322168/1‑141 (MQ=255)                                                                                                                                   aaataataCACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGt            <  1:266454/140‑1 (MQ=255)                                                                                                                                       aataCACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAAc        <  1:337492/141‑1 (MQ=255)                                                                                                                                          acacGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGat     >  2:192547/1‑141 (MQ=255)                                                                                                                                            acGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGatat   >  1:385041/1‑141 (MQ=255)                                                                                                                                             cGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGATAtt  >  2:388041/1‑141 (MQ=255)                                                                                                                                             cGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGATAtt  >  2:104748/1‑141 (MQ=255)                                                                                                                                              |                                                                                                                                            AGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATGAGATAGTTATAAAAGAAGATTCATATAATCCATTCGTAACGAAAACATCTGAAAGTTTAATAGCTGATGAT‑GAATCTTCTGGTTATAATAATACACGTGAAAAAGATGAAGACTACTTCAAAAAACAACAAGAAATTTTACAAGAAATGGATCAAACATTTGATTCAAATGATGGTACAACTGTGCAAAATTATGAGAATAAAGCGTCTGATGATTATTATGATGTAAACGATATT  >  USA300TCH1516_ALE/1324347‑1324626

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: ‑