BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	28.3%	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	28.3%	62.8 / 17.1	41	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand): ref base C (14/15); new base A (8/4); total (22/19)
Fisher's exact test for biased strand distribution p-value = 3.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111377‑111651

tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                         <  1:205541/140‑1 (MQ=255)

       gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  1:261481/1‑140 (MQ=255)

        ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATAGATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                 >  1:182987/1‑140 (MQ=255)

          aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                               >  1:211503/1‑140 (MQ=255)

                 aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAACTAat                                                                                                                        >  1:13742/1‑140 (MQ=255)

                  aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                       >  2:242760/1‑140 (MQ=255)

                   aaCATAAAAAAAGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGACTTATAAAGATGGAGATATATCATATAATCCAGCGGTGCCGAGTTATTTAGCTCAATATTAATTAACTAatga                                                                                                                      >  1:72191/1‑140 (MQ=21)

                    aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                     >  1:212024/1‑140 (MQ=255)

                     cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                    >  1:118599/1‑140 (MQ=255)

                        aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                 <  1:286750/140‑1 (MQ=255)

                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATta                                                                                                                >  1:129246/1‑140 (MQ=255)

                            aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             >  2:98546/1‑140 (MQ=255)

                             aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            <  1:162415/140‑1 (MQ=255)

                                    cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     <  2:50454/140‑1 (MQ=255)

                                       taaCTTTTAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:288968/139‑1 (MQ=255)

                                       aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCTGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:139443/140‑1 (MQ=255)

                                       aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:289059/140‑1 (MQ=255)

                                       aaaCTTTAAGTTGTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:206922/140‑1 (MQ=17)

                                          cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               >  1:206636/1‑140 (MQ=255)

                                          cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTACTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               <  2:205680/140‑1 (MQ=255)

                                            ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  2:9414/140‑2 (MQ=255)

                                             tAAGTTTTTTGCGCAATATAGCAATTTTAAAGCTTTCATGAATGATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  1:59384/140‑1 (MQ=255)

                                             tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  2:250827/140‑1 (MQ=255)

                                               aGTTTATTGTGCAATATCGCAATTTTAAAGAGTTAATGAAATATAAAGATGGAGATATATCATATAGTCCAGAGGTGCCGAGTTATTCGGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                          >  1:235632/1‑140 (MQ=17)

                                                gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                         <  1:254574/140‑1 (MQ=255)

                                                       gcgcAATATAGCAATTTTAAAGCTATACTAGTTGATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGCTGATTATAATGTAAAACAATTACGTAAAAGAAATGa                                                                                  >  1:76510/1‑140 (MQ=17)

                                                       gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                  <  2:312266/140‑1 (MQ=255)

                                                              ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCTAATCTCACTAAAAGGTGACGAAAGCTACTGCTAAATATCAATTAACTACTGATAATTAGAATGTGAAACAATTACGCAAAAGATATGATATAccg                                                                           >  1:75497/1‑139 (MQ=9)

                                                                         aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAGCAAATAAAgc                                                                <  1:234543/140‑1 (MQ=255)

                                                                          aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCACCGAGTAAAgcg                                                               >  2:223163/1‑140 (MQ=11)

                                                                                         gtaAAGAGTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttcttg                                                <  1:229947/139‑1 (MQ=255)

                                                                                            aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                             >  2:196398/1‑140 (MQ=255)

                                                                                                        tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACACATAAAGCGCCGAAGCTGTTGTTGAAGGGAACAGGGaaa                                 >  2:76053/1‑139 (MQ=255)

                                                                                                         atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                                <  2:162485/140‑1 (MQ=255)

                                                                                                          tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTATAAGCTTTACGTACAAGATACTACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  1:315454/140‑1 (MQ=17)

                                                                                                             tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                            >  2:35810/1‑140 (MQ=255)

                                                                                                                     agatGTGCCGAGTTATTTAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAATGTACAGCGAATTTAAAAGGTtcat                    <  2:72191/140‑1 (MQ=17)

                                                                                                                         gTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATAATAATGTAAAACAATTACGCAAAAGATATGCTATAACAAAAAATAAAGCGCCGAAGCTATTGTTAAAAAGTACAGAGAATTTAAAAGGTTCATCAGt                >  2:104346/1‑140 (MQ=11)

                                                                                                                          tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  2:172516/1‑140 (MQ=255)

                                                                                                                            ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg             >  2:182099/1‑140 (MQ=255)

                                                                                                                                     tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa    <  1:196398/140‑1 (MQ=255)

                                                                                                                                       aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGACAGGTACAGGGAATTTAAAAGGTTCCTCAGTTCGACATgaaaaaa  >  1:319764/1‑140 (MQ=17)

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111377‑111651

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: `‑`