BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,177,523	T→C	19.6%	F332F (TTT→TTC)	sppA →	protease IV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,177,523	0	T	C	19.6%	204.0 / 35.9	137	F332F (TTT→TTC)	sppA	protease IV
Reads supporting (aligned to +/- strand): ref base T (39/71); new base C (15/12); total (54/83)
Fisher's exact test for biased strand distribution p-value = 7.79e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 138 total aligned reads displayed.

ATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGC  >  minE/1177458‑1177585

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:1070341/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:2184105/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:2132269/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:1000946/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:1991450/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:2550961/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:1973866/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:2763014/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:2830055/69‑1 (MQ=255)

aTCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:814770/69‑1 (MQ=255)

 tCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             <  1:818767/68‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:1141107/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:1304779/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:3433976/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:1333384/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:764706/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:1221725/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:2972594/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:1745455/69‑1 (MQ=255)

      tattaCGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:2915486/69‑1 (MQ=255)

       attacgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:3278344/68‑1 (MQ=255)

       attacgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             >  1:2274067/1‑62 (MQ=255)

       attacgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCt                                                             >  1:1417359/1‑62 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:1664782/68‑1 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:1244052/68‑1 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:1581103/68‑1 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:1526201/68‑1 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:1369973/68‑1 (MQ=255)

            gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  <  1:3306177/68‑1 (MQ=255)

             attacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTa                                                <  1:2676117/69‑1 (MQ=255)

             attacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTa                                                <  1:2319772/69‑1 (MQ=255)

             attacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTa                                                <  1:2304779/69‑1 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCttt                                                                >  1:1387150/1‑43 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCaa                                                   >  1:4118/1‑56 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  >  1:1707013/1‑57 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  >  1:2846850/1‑57 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  >  1:555986/1‑57 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  >  1:1285328/1‑57 (MQ=255)

                       gAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAAt                                                  >  1:1261046/1‑57 (MQ=255)

                          aaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGa                                   <  1:2411518/69‑1 (MQ=255)

                          aaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGa                                   <  1:486973/69‑1 (MQ=255)

                          aaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGa                                   <  1:1426895/69‑1 (MQ=255)

                           aCGCCGGCAGATACCGGTGACAGTATCGGTGTCGTCTTCGCTAATGgc                                                       <  1:2952099/48‑1 (MQ=39)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:64268/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:188115/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:1292716/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:2973358/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:1392034/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTatggat                                           <  1:3347094/48‑1 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:1757878/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:3266099/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:2420575/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:2440241/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:2999348/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:2110966/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:110015/1‑69 (MQ=255)

                                       aCCGGTGACAGCATCGGTGTCGTATTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAAt                      >  1:2964053/1‑69 (MQ=255)

                                                aGCATCTGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGt             <  1:2268013/69‑1 (MQ=255)

                                                aGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGt             <  1:3292934/69‑1 (MQ=255)

                                                aGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGt             <  1:2948368/69‑1 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:2915441/69‑1 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:2841074/69‑1 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          >  1:2822096/1‑69 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:639793/69‑1 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:1355744/69‑1 (MQ=255)

                                                   aTCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:2246412/69‑1 (MQ=255)

                                                    tCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGAt          <  1:2470546/68‑1 (MQ=255)

                                                     cGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATAc        <  1:394968/69‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGa                                   <  1:179744/41‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:2763018/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:2465608/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:3030081/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:761192/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:1160434/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:23353/64‑1 (MQ=255)

                                                      ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTg            <  1:1157400/64‑1 (MQ=255)

                                                       gtgtCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGTAACTCAGGGGAATGTTGGCGGTg            <  1:1700866/63‑1 (MQ=255)

                                                         gtcgtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCAc     >  1:2896721/1‑68 (MQ=255)

                                                         gtcgtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACt    >  1:2828058/1‑69 (MQ=255)

                                                         gtcgtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCAc     >  1:2049374/1‑68 (MQ=255)

                                                         gtcgtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACt    >  1:183263/1‑69 (MQ=255)

                                                         gtcgtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACt    >  1:2541189/1‑69 (MQ=255)

                                                          tcgtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTg   >  1:2948754/1‑69 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:1273154/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:1229809/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:24194/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:664813/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:2177329/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:812425/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:2020175/1‑68 (MQ=255)

                                                            gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:240368/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGt                    >  1:885544/1‑50 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:699027/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:889492/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:2271489/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:714381/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:1329676/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:1979637/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:528849/1‑68 (MQ=255)

                                                            gtcTTCGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGc  >  1:2242104/1‑68 (MQ=255)

ATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGC  >  minE/1177458‑1177585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`