Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	552,627	G→A	36.6%	R299R (CGC→CGT)	ybiW ←	predicted pyruvate formate lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	552,627	0	G	A	36.6%	63.8 / 59.3	98	R299R (CGC→CGT)	ybiW	predicted pyruvate formate lyase
Reads supporting (aligned to +/- strand): ref base G (19/43); new base A (24/12); total (43/55)
Fisher's exact test for biased strand distribution p-value = 7.13e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 139 total aligned reads displayed.

GCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGATACTGAGTGACCGTTAGATTCGA  >  minE/552563‑552694

gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1475864/1‑69 (MQ=255)

gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1863799/1‑69 (MQ=255)

gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1077876/1‑69 (MQ=255)

  cagcagCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGa                                                               <  1:2482425/69‑1 (MQ=255)

       gcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:1692904/69‑1 (MQ=255)

       gcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          >  1:1046834/1‑69 (MQ=255)

       gcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2520088/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:1667705/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:1967663/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:2034262/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:1310733/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:2343482/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:2384340/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:3013567/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:519068/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:52555/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:65499/69‑1 (MQ=255)

        cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:65848/69‑1 (MQ=255)

         tATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:104371/68‑1 (MQ=255)

          aTGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAg                                                            <  1:2179043/64‑1 (MQ=255)

           tGCAGCATCTCGATGGCGTGTTCGCGATCGAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                                         <  1:3424823/66‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGt                                                           >  1:2116811/1‑62 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2722611/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:3270544/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2478387/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:121731/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2699647/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2819501/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:1183604/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                                          <  1:2928884/63‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:1858812/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:3043837/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:2772418/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:360069/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:3068446/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:2919035/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                                      >  1:796820/1‑67 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                                                    <  1:732180/69‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                                                    <  1:336475/69‑1 (MQ=255)

             cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                                                    <  1:2039974/69‑1 (MQ=255)

              agcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                                                    <  1:2187334/68‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:2617680/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:3113074/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:2902357/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:3008872/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:2733872/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:2955745/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:2996911/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:1293681/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:1519392/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:972178/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1515496/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:897587/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 <  1:1930010/52‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1956185/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:1030900/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:2067243/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                                                 >  1:43385/1‑52 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAgaga                                                <  1:311646/69‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAgaga                                                <  1:2266969/69‑1 (MQ=255)

                 aTCTCGATGGCGTGTTCGCGATCCAGCGTATGGTTGAGTTCAACGTCgcggc                                                                 <  1:1481955/52‑1 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATagag                                                 >  1:1814285/1‑59 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGAt                                               >  1:3182202/1‑61 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTgtt                                         >  1:2258843/1‑65 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:111101/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:731751/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:771867/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:3270680/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:987987/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:285360/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:1431766/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:1878207/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:1412836/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:1404161/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:1306149/1‑68 (MQ=255)

                          gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                                        >  1:2672397/1‑68 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGATATACTGGTCCATAc                                   <  1:557936/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGTTACTGGTCCATAc                                   <  1:1059807/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:1761593/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:3220422/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:92417/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:2251906/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:2104811/69‑1 (MQ=255)

                              gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:25562/69‑1 (MQ=255)

                               ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:2468129/68‑1 (MQ=255)

                               ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:2540282/68‑1 (MQ=255)

                               ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:680714/68‑1 (MQ=255)

                               ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc                                   <  1:570488/68‑1 (MQ=255)

                               ttCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACg                                  <  1:1737838/69‑1 (MQ=255)

                                 cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa                                 >  1:2320135/1‑68 (MQ=255)

                                 cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa                                 >  1:3048753/1‑68 (MQ=255)

                                 cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa                                 >  1:1570941/1‑68 (MQ=255)

                                 cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa                                 >  1:1857697/1‑68 (MQ=255)

                                   cgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAg                                                            <  1:1053933/39‑1 (MQ=255)

                                          gCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGAt                        <  1:825260/68‑1 (MQ=255)

                                                         cAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGa                         <  1:3181928/52‑1 (MQ=255)

                                                         cAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGa                         <  1:1553478/52‑1 (MQ=255)

                                                         cAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGATACTGAGTGAc              >  1:2423510/1‑63 (MQ=255)

                                                               cgcgGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGATACTGAGTGACCGTTAGATTCGa  <  1:2949840/69‑1 (MQ=255)

                                                                gcggcgATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGATACTGAGTGACCGTTAGATTCGa  <  1:1196037/68‑1 (MQ=255)

GCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGATACTGAGTGACCGTTAGATTCGA  >  minE/552563‑552694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A