BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,560	T→C	9.4%	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	9.4%	111.9 / 2.1	41	R210R (CGT→CGC)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand): ref base T (24/13); new base C (2/2); total (26/15)
Fisher's exact test for biased strand distribution p-value = 6.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACT  >  USA300TCH1516_ALE/111425‑111698

gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAg                                                                                                                                       >  1:489668/1‑141 (MQ=255)

   ttttGCGCAATATAGCAATTTTAATTTTTTAATTAATTCCCTCGCCAGATGAATAGCAGATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                                                                    <  1:629337/141‑1 (MQ=14)

   ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                                                                    <  1:514511/141‑1 (MQ=255)

   ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                                                                    <  1:514287/141‑1 (MQ=255)

      tGCGCAATATAGCAATTTTAAAGATTAAATGAATTATAAAGAATGAGATAAATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                                                                 <  1:419259/141‑1 (MQ=14)

         gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATTATGATTATAATGTAAACAAATTAAGCAAAAGatataatat                                                                                                                              >  1:33399/1‑136 (MQ=17)

                  cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGAGATGGTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacgag                                                                                                                     <  1:633716/141‑7 (MQ=11)

                   aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcaaacaaaa                                                                                                                    >  1:800136/1‑140 (MQ=255)

                    aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATa                                                                                                                   <  1:782155/141‑1 (MQ=255)

                      tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaa                                                                                                                 >  1:185283/1‑141 (MQ=255)

                                 aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAGGCt                                                                                                      >  1:283433/1‑141 (MQ=255)

                                 aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAACt                                                                                                      >  1:259248/1‑141 (MQ=255)

                                  aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                                                                     >  1:32163/1‑141 (MQ=255)

                                  aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                                                                     >  1:728558/1‑141 (MQ=255)

                                   tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                                                                    <  1:185902/141‑1 (MQ=255)

                                   tGAAGTATAAAGATGGCGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                                                                    <  1:33014/141‑1 (MQ=255)

                                               aTGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTa                                                                                        <  1:600545/141‑1 (MQ=255)

                                                tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAc                                                                                       >  1:792677/1‑141 (MQ=255)

                                                     atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                                  >  1:140966/1‑141 (MQ=255)

                                                       atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAt                                                                                >  1:481854/1‑141 (MQ=255)

                                                           cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCCAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                                                            >  1:765766/1‑141 (MQ=255)

                                                                    cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATAATAATTATAATGTAAAACTATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAATGTACAGGGAATTTAAAAGGTtcat                                                                   >  1:381457/1‑141 (MQ=255)

                                                                       agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                                                                >  1:721654/1‑141 (MQ=255)

                                                                        ggTGCCGAGTTATTCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACACTTACGTAAAAGATATGCCATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGAACAGGGAAAATAAACGGCTcagcaga                                                               >  1:384786/1‑140 (MQ=18)

                                                                           gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg                                                            >  1:40647/1‑141 (MQ=255)

                                                                             cGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGat                                                          >  1:671457/1‑141 (MQ=255)

                                                                              gAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata                                                         <  1:304531/141‑1 (MQ=255)

                                                                               aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat                                                        >  1:536166/1‑141 (MQ=255)

                                                                               aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat                                                        >  1:55827/1‑141 (MQ=255)

                                                                                           cAATAGTAATTACTTAAAGACGATTATAAGGTAAAACAATTACGTAAAAGATATCACATACCAAAAAAAAAAGATCCGAAGCGGTTGGTGTAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGaa                                            <  1:309252/141‑1 (MQ=14)

                                                                                              tatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAttt                                         >  1:270978/1‑141 (MQ=255)

                                                                                                   aTTAACTAATGATGATAATGATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACttt                                    >  1:485879/1‑141 (MQ=255)

                                                                                                                      aaTGTAAAACAATTGCGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaa                 >  1:568408/1‑141 (MQ=255)

                                                                                                                         gTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTTATCAGGGAGATGGAAAAAAATTGACTTTACTTTGTTAGAGAATAAAAATGaaatt              >  1:409410/1‑139 (MQ=18)

                                                                                                                         gTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGGTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTTAATTTACTTTTTTAGAGAATAAAAATGAAAat              >  1:725375/1‑141 (MQ=255)

                                                                                                                          tAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAata             <  1:862709/141‑1 (MQ=255)

                                                                                                                          tAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGATGAACAGCACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAata             <  1:412920/141‑1 (MQ=255)

                                                                                                                             aaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTATAGGGAATGTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAttt          <  1:857975/141‑1 (MQ=255)

                                                                                                                              aCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTAATATCGTATAAGAATAAAAATGAAAATAttta         <  1:208234/141‑1 (MQ=17)

                                                                                                                                aaTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATCTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttact       >  1:696504/1‑141 (MQ=255)

                                                                                                                                     cGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATttactttact  >  1:213370/1‑141 (MQ=255)

GTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACT  >  USA300TCH1516_ALE/111425‑111698

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: `‑`