Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,560	T→C	9.7%	R210R (CGT→CGC)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,560	0	T	C	9.7%	121.8 / 3.6	50	R210R (CGT→CGC)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (29/15);  new base C (3/2);  total (32/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTGA  >  USA300TCH1516_ALE/111423‑111700                                                                                                                                           |                                                                                                                                              aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                                                                            <  1:219038/141‑1 (MQ=255) aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaa                                                                                                                                            >  2:307410/1‑141 (MQ=255)    ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                                                                         >  1:457985/1‑141 (MQ=255)        ttGCGCAATATAGCACTTTTAAAGATCTAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCTGCTA‑ACTATCAATAAACTAATGATGATTATAATGTAATACAATTACGCAAAAGATATg                                                                                                                                     <  1:372149/141‑1 (MQ=17)          gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGaa                                                                                                                                   >  1:482008/1‑140 (MQ=255)             cattataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACATTTCCGTAACAGATATTACAtt                                                                                                                                >  2:180524/4‑140 (MQ=18)             cAATATAGCAATTTTAAAGCTTTAATGCATTATAAAGATAGAGATATATCATATAATCCGGATGTGCCTATTTATTCGACTA‑ACTATCAATTAACTAATGATGATTGTCATCTAAAAAAATTAAGCAACatatattatatc                                                                                                                                >  2:174081/1‑135 (MQ=9)             cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATa                                                                                                                                >  2:58867/1‑141 (MQ=255)               atatAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTA‑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)                                                                                                aaTATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAt                                             >  2:560185/1‑141 (MQ=255)                                                                                                 atatCAATTAACTAATGATGATTATACTGTAAAACTATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCGGTTGATGCAAGGTACAGGGAAGTTAAAAGGTACATCCGTTGGATATAAAAAAAGTgcagt                                            >  1:296040/1‑137 (MQ=14)                                                                                                 atatCAAGGAGCGAATGATGATTATAATGTAAAACAAGGACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTGGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAtt                                            <  1:580929/141‑1 (MQ=17)                                                                                                  tatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAttt                                           >  2:566461/1‑141 (MQ=255)                                                                                                    acAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTAc                                         <  1:357677/140‑1 (MQ=255)                                                                                                     aaaTTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTatt                                        <  2:98960/140‑3 (MQ=255)                                                                                                           aCTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAT‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTa                                  <  1:568601/141‑1 (MQ=255)                                                                                                           aCTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTa                                  <  1:192930/141‑1 (MQ=255)                                                                                                               atgatgATTGTAATGTAAAACAATTACGTAAAAGATATGACATAC‑CGACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAgaga                              <  2:517505/141‑1 (MQ=255)                                                                                                                tgatgaTTATAATGTAAAACAATTACGTAACAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGGTCATCAGTTGGATATAAAAAAATTGAATTTAATTTTTTagcaaa                             >  2:461084/1‑137 (MQ=255)                                                                                                                tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                             >  1:27345/1‑141 (MQ=255)                                                                                                                tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                             >  1:27339/1‑141 (MQ=255)                                                                                                                tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                             >  2:105028/1‑141 (MQ=255)                                                                                                                tgatgaTTATAATGTAAAAAAATTACGTAAAAGATATGACAAAC‑AAACAAATAACGCTCAGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGATGGATCTCAACACATTGAATGTACTTTTTTTgagag                             >  1:27344/1‑140 (MQ=14)                                                                                                                 gatgatTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAAt                            >  1:35790/1‑141 (MQ=255)                                                                                                                        ataATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGGATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAGTTTACTGTGTTAGAGGATAAAGATg                     >  1:354689/1‑141 (MQ=17)                                                                                                                          aaTGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAATTAAAAGGGTCATCAGTTGGAAATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaa                   >  2:168727/1‑141 (MQ=255)                                                                                                                                aaaCAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtt             >  1:577612/1‑141 (MQ=255)                                                                                                                                   cAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAACAtttac          >  2:91469/1‑141 (MQ=255)                                                                                                                                         cGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATttactttact    <  2:353839/141‑1 (MQ=255)                                                                                                                                         cGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATttactttact    >  1:26721/1‑141 (MQ=255)                                                                                                                                           tAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTGGGGAATTAAAATGGAAATATTTACTTTACTgg  >  1:220168/1‑140 (MQ=255)                                                                                                                                           tAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTGa  >  1:220638/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                              AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTC‑AATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAC‑CAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACTGA  >  USA300TCH1516_ALE/111423‑111700

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: ‑