Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	28.3%	S194S (TCA→TCG)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,512	0	A	G	28.3%	79.7 / 35.6	58	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (23/18);  new base G (9/7);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111373‑111650                                                                                                                                              |                                                                                                                                             cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                             <  1:272559/141‑1 (MQ=255)  tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGc                                                                                                                                            >  1:500760/1‑141 (MQ=255)   aCTGAGGAAGTTAAAGAAGAAAATATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCt                                                                                                                                           <  1:75998/141‑1 (MQ=255)      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                                                                                                                    <  1:506655/141‑1 (MQ=255)                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAatgatg                                                                                                                    >  2:273184/1‑141 (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)                                                                                                                                              |                                                                                                                                             CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAAT‑AT‑AGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAA  >  USA300TCH1516_ALE/111373‑111650

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: ‑