Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	27.8%	Q196K (CAA→AAA)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,516	0	C	A	27.8%	82.3 / 28.4	54	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (23/16);  new base A (7/8);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 5.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111378‑111650                                                                                                                                             |                                                                                                                                         gAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTa‑aa                                                                                                                                       >  2:95835/1‑141 (MQ=255)     aaGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATGCCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATc                                                                                                                                   >  1:568223/1‑141 (MQ=255)      aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGTGTGAAAGAGAGCATGTAGACCAGATGGGCCGAGCTATTCGGCTA‑AATATCa                                                                                                                                  >  1:138481/1‑141 (MQ=21)      aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCa                                                                                                                                  >  2:233580/1‑141 (MQ=255)         tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTCGCATT‑AT‑AGCAATTATAAAGAGTTAATGAATTATAAAGATGGAGATATATCATATAATCTAGGGGTTCCGAGTTATTCAGCTC‑AATATAAAtt                                                                                                                               >  2:357677/1‑141 (MQ=21)          aaaagagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTGTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGGCCCGAGTTACTCGGCTA‑AATATCAATTa                                                                                                                              <  2:558601/136‑1 (MQ=17)          aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTa                                                                                                                              <  2:304687/141‑1 (MQ=255)           aagaagAAAACATAACAAAAGAAATCGCAAACTTTACGTTTTTTGCGCGATAATAATCGGTTTTTCAG‑‑TAAATGAATTATAAAGTTGGTCTTTTAGCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTaa                                                                                                                             <  2:430621/141‑1 (MQ=16)             gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACt                                                                                                                           <  2:500760/141‑1 (MQ=255)              aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTa                                                                                                                          <  1:350757/141‑1 (MQ=255)                gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAat                                                                                                                        <  1:169295/141‑1 (MQ=255)                 aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGCAGTGCCGAAGTATGCAGCTC‑AATATCAATTAACTAata                                                                                                                       >  2:457125/1‑140 (MQ=21)                   aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCCGAGGTGCCGAGTTATTCGGCTA‑AATATAAATTAACTAatgat                                                                                                                     >  1:14870/1‑141 (MQ=255)                    aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAatgatg                                                                                                                    >  2:273184/1‑141 (MQ=255)                    aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAatgatg                                                                                                                    <  1:506655/141‑1 (MQ=255)                     cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAAtgatga                                                                                                                   >  1:496227/1‑141 (MQ=255)                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATtat                                                                                                               <  2:326923/141‑1 (MQ=255)                            aaaGAAATCGAAAACTTTAAGTTTTTTTTTTTTT‑TT‑TTCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAAt                                                                                                            >  2:568601/1‑141 (MQ=17)                               gAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTa                                                                                                         <  2:459280/141‑1 (MQ=255)                                aaaTCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAAATCTTGATGATTATAATGTaa                                                                                                        <  2:308829/141‑1 (MQ=18)                                   acGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     <  2:200191/140‑1 (MQ=255)                                    cGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  1:123301/1‑141 (MQ=255)                                     gagtgcTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   >  2:527655/6‑141 (MQ=255)                                     gAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAACCCAGAGGCGCCGAGTTAGACGGCGA‑AATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  2:431406/141‑1 (MQ=17)                                     gAAAACTTTAAGTTTTTCGCGCAAT‑AT‑AGCAACATTAAAGATTTAATGAATTATAAAGATGGAGATATATCATCTAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATACAAATTCCCTACTGATGATTATAATGTAAACCaa                                                                                                   >  2:580929/1‑141 (MQ=18)                                          ctgtAAGGTTTTTGCGCAAT‑AT‑AGCAATTTTGAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCGC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                              <  2:51693/138‑1 (MQ=255)                                              aaGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                          <  1:219038/141‑1 (MQ=255)                                              aaGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaa                                                                                          >  2:307410/1‑141 (MQ=255)                                                 ttttttGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                       >  1:457985/1‑141 (MQ=255)                                                     ttGCGCAAT‑AT‑AGCACTTTTAAAGATCTAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCTGCTA‑ACTATCAATAAACTAATGATGATTATAATGTAATACAATTACGCAAAAGATATg                                                                                   <  1:372149/141‑1 (MQ=17)                                                       gcgcAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGaa                                                                                 >  1:482008/1‑140 (MQ=255)                                                          catt‑at‑aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACATTTCCGTAACAGATATTACAtt                                                                              >  2:180524/4‑140 (MQ=18)                                                          cAAT‑AT‑AGCAATTTTAAAGCTTTAATGCATTATAAAGATAGAGATATATCATATAATCCGGATGTGCCTATTTATTCGACTA‑ACTATCAATTAACTAATGATGATTGTCATCTAAAAAAATTAAGCAACatatattatatc                                                                              >  2:174081/1‑135 (MQ=9)                                                          cAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATa                                                                              >  2:58867/1‑141 (MQ=255)                                                            at‑at‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAAATATGATATAc‑c                                                                           >  2:409294/1‑141 (MQ=14)                                                                   gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATGCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATTATGATGATAATGTAAAACAATTACGTAAAAGATATGACATAC‑caacaa                                                                      >  1:318573/1‑141 (MQ=255)                                                                          tAAAGATTTAATGAATTATAAAGATGGATATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAgc                                                               <  1:348577/141‑1 (MQ=255)                                                                            aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAgcgc                                                             >  1:40986/1‑141 (MQ=255)                                                                                   aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCt                                                      <  2:406040/141‑1 (MQ=255)                                                                                    aTGAATCATCAAGATGGAGATATATCATATAATCCACAGGTGCCAAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCtg                                                     <  1:14333/141‑1 (MQ=255)                                                                                          tataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTCTGCA‑CTCGAATAGCAAGTAACTAATGATGATTATAATGTCAAACAATTACGTCAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCtgttgtgg                                               >  2:68837/1‑139 (MQ=17)                                                                                               aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                          <  1:233580/141‑1 (MQ=255)                                                                                                    gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                     >  2:577454/1‑141 (MQ=255)                                                                                                     agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                    >  1:502760/1‑141 (MQ=255)                                                                                                          tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                               <  1:273184/141‑1 (MQ=255)                                                                                                           atCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTACATCATGCATATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                              <  1:416476/141‑1 (MQ=17)                                                                                                               tataATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaaa                          >  2:375369/1‑141 (MQ=255)                                                                                                                  aaTTCAGAGGGGGCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACACTTCTGGCGAAGAGATGA‑ATGCTGAACGGAGAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                       <  1:293812/141‑1 (MQ=12)                                                                                                                    tCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                     <  1:527655/141‑1 (MQ=255)                                                                                                                     ccAGAGGAGCCGAGTTATTCAGCTC‑AACATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                    <  2:399062/141‑1 (MQ=255)                                                                                                                           gTGCCGAGTTATTCAGCTC‑AATATCAATCAACTAATGATGATTATACTGAAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt              >  2:128778/1‑141 (MQ=255)                                                                                                                            tGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTGTAATGTAAAACAATTACGTAAAAGATATGACATAC‑CGACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTg             >  1:517505/1‑141 (MQ=255)                                                                                                                              ccGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAACGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa           >  1:224273/1‑141 (MQ=255)                                                                                                                                     aTTCAGCTC‑AATATCAAGTAACTAATGATAATTATAATGTAAAACAATTACGTAGTAGATATGACATAC‑CAACAAGTAAAGCGCCGAAGCTGTTGGGGGGCGATCCAGGGAACGTAAGATGTTGATCCGTGGGATAGaaaa    >  2:578794/1‑141 (MQ=12)                                                                                                                                       tCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCAACAGTTGGATATaaaaaa  >  1:530392/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                         GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111378‑111650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑