BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	30.8%	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	30.8%	54.7 / 26.3	39	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand): ref base A (13/14); new base G (3/9); total (16/23)
Fisher's exact test for biased strand distribution p-value = 2.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

ACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111375‑111651

aCTGAGGAAGTTAAAGAAGAAACCATAAAAAAAGAAACCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCt                                                                                                                                          <  1:82859/141‑1 (MQ=255)

 atGAGCAAGTTAAAGAAGAAAACAGAAAAAAAGAAATCGAAAACTTTAAGTTATTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCta                                                                                                                                         <  2:50934/140‑2 (MQ=18)

     ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATGAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  2:177456/141‑1 (MQ=255)

     ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  2:151734/141‑1 (MQ=255)

               aaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                           <  2:160449/140‑1 (MQ=255)

                 agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCACAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                         <  2:240386/141‑1 (MQ=255)

                    aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAAATTTAAGAAGCAAAGGAAGTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                      <  1:72341/141‑1 (MQ=14)

                      aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAAGTGCCGAGTTATTAGGCTAAATATCAATTAACTAatgatg                                                                                                                    >  2:212148/1‑141 (MQ=255)

                         aaaaaaaaGAAATCGAAAAGTTTAAGTTTTTTGCGCAATATAGGAATTTTAAAGATTTAATGAATTATAAAGATGTAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                 <  2:296454/140‑1 (MQ=255)

                           aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTGAGCTCAATATCAATTAACTAATGATGATtat                                                                                                               >  2:141666/1‑141 (MQ=255)

                                 gAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                                                         >  1:125722/1‑141 (MQ=255)

                                  agaTCGAAAACTTGAAGTTTTTTGCGCAATATAGCAAGTTTAAATATTTAAGGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                        <  2:134960/139‑1 (MQ=14)

                                   aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGATATTCAGCTCAATATCAATTAACTAATACTGATTATAATGTaaa                                                                                                       >  2:102989/1‑141 (MQ=255)

                                    aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                      >  1:121161/1‑141 (MQ=255)

                                     tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     >  1:148543/1‑141 (MQ=255)

                                         aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                 >  1:66488/1‑141 (MQ=255)

                                         aaaCTTTAAGTTTTATGCGGAGTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                 <  2:217788/141‑1 (MQ=255)

                                               tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                           <  1:136500/141‑1 (MQ=255)

                                                 aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                         <  1:220946/141‑1 (MQ=255)

                                                  gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAg                                                                                        <  1:35533/141‑1 (MQ=255)

                                                  gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                                        <  1:59894/141‑1 (MQ=255)

                                                       ttGCGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATg                                                                                   <  1:82600/141‑1 (MQ=255)

                                                          ggcAATATAGGAATTGTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATggta                                                                                <  2:2500/140‑4 (MQ=14)

                                                           gcAATAGAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAt                                                                               <  2:37416/141‑1 (MQ=255)

                                                               aagaacAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                           <  2:175958/136‑2 (MQ=11)

                                                                       ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                   <  2:110770/141‑1 (MQ=255)

                                                                         ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACGGAGTTATTAAGCTCGATATCAGTTAACTAATGATGATTTTAATGTAAAACAATTACGTAAAATATAAGACATACCAACAAATaaaa                                                                 >  2:94744/1‑140 (MQ=21)

                                                                          tAAAGATTTAATGAATTATAAAGATGAAGATATATAATATAATCCAGAGGTACCGAGTTATTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAAATATGATAAACAAACTAGTaaaaa                                                                >  2:172823/1‑139 (MQ=14)

                                                                            aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcgc                                                              >  1:288842/1‑141 (MQ=255)

                                                                                    aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                      <  2:258329/141‑1 (MQ=255)

                                                                                         ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                 <  2:148543/141‑1 (MQ=255)

                                                                                                              atatAATCCAGAGGTGCCGAGTCATTCAGCTCAATATCAATTAACTAATGATGAGTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTTTTGAAAGGTACAGGGAATTTaaa                            <  1:141666/141‑1 (MQ=255)

                                                                                                              aaataATTCAGGGGTGCAGAGTTATTCAGCTCAATAGCAAGTAACTAATGAGGATTATAATGTAAAACAATTACGAAAAAGATAGGACATACCAACATATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                            <  2:119122/139‑1 (MQ=18)

                                                                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                  >  1:183741/1‑141 (MQ=255)

                                                                                                                             gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg             >  2:94836/1‑141 (MQ=255)

                                                                                                                                 aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat         >  1:77301/1‑141 (MQ=255)

                                                                                                                                     aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa     >  1:199094/1‑141 (MQ=255)

                                                                                                                                     aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa     >  1:198964/1‑141 (MQ=255)

                                                                                                                                        cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGAAGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  >  1:71395/1‑141 (MQ=255)

ACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111375‑111651

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: `‑`