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 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,874,329	A→G	37.7%	I191T (ATT→ACT)	ygcF ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,874,329	0	A	G	37.7%	116.8 / 154.9	138	I191T (ATT→ACT)	ygcF	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (46/40); new base G (42/10); total (88/50)
Fisher's exact test for biased strand distribution p-value = 1.73e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

Only 100 of 145 total aligned reads displayed.

TCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTCAAT  >  minE/1874261‑1874399

tCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATc                                                                      <  1:2863180/71‑1 (MQ=255)

tCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATc                                                                      <  1:1078344/71‑1 (MQ=255)

tCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATc                                                                      <  1:3739725/71‑1 (MQ=255)

     aaaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTg                                                                 <  1:1162379/71‑1 (MQ=255)

     aaaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTg                                                                 <  1:2934555/71‑1 (MQ=255)

     aaaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTg                                                                 <  1:1375866/71‑1 (MQ=255)

     aaaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTg                                                                 <  1:3622794/71‑1 (MQ=255)

     aaaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTg                                                                 <  1:1395439/71‑1 (MQ=255)

      aaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTg                                                                 >  1:2819419/1‑70 (MQ=255)

      aaCGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGc                                                                <  1:694954/71‑1 (MQ=255)

         gCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCATCCTTTTGGCTAGTCGGCTg                                                                 >  1:2141454/1‑70 (MQ=255)

         gCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCATCCTTTTGGCTAGTCGGCTg                                                                 >  1:1875691/1‑70 (MQ=255)

         gCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCATCCTTTTGGCTAGTCGGCTg                                                                 >  1:3108766/1‑70 (MQ=255)

         gCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCATCCTTTTGGCTAGTCGGCTg                                                                 >  1:157799/1‑70 (MQ=255)

          ccAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAAt                                                                       >  1:3472700/1‑60 (MQ=255)

            aaTTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCa                                                          <  1:2263923/71‑1 (MQ=255)

               tACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAAt                                                        >  1:2139884/1‑70 (MQ=255)

                aCGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGa                                                      >  1:2537641/1‑71 (MQ=255)

                aCGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGa                                                      >  1:1618336/1‑71 (MQ=255)

                aCGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGa                                                      >  1:4078306/1‑71 (MQ=255)

                aCGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGa                                                      >  1:445991/1‑71 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCaa                                                         >  1:6143/1‑58 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCaa                                                         >  1:1834886/1‑58 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCaa                                                         >  1:646792/1‑58 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:949971/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:2030212/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:2420248/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:3081454/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:3370645/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:3441634/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:3451225/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAAt                                                        >  1:3912141/1‑59 (MQ=255)

                          cAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGttt                                            <  1:3526273/71‑1 (MQ=255)

                            ggTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAAt                                                        <  1:2879911/57‑1 (MQ=255)

                            ggTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAAt                                                        <  1:294484/57‑1 (MQ=255)

                            ggTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAAt                                                        <  1:2640107/57‑1 (MQ=255)

                               ttCAATGCACAAACGTGTTG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatcat                                       >  1:2950983/1‑71 (MQ=255)

                               ttCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTatcat                                       >  1:2507915/1‑71 (MQ=255)

                               ttCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGa                                                      >  1:1833388/1‑56 (MQ=255)

                               ttCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGa                                                      >  1:2377141/1‑56 (MQ=255)

                               ttCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatcat                                       >  1:3193551/1‑71 (MQ=255)

                               ttCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        >  1:2474192/1‑70 (MQ=255)

                                  aaTGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        <  1:2483081/67‑1 (MQ=255)

                                  aaTGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        <  1:3074936/67‑1 (MQ=255)

                                  aaTGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        <  1:729860/67‑1 (MQ=255)

                                  aaTGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        <  1:2350552/67‑1 (MQ=255)

                                  aaTGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        <  1:813945/67‑1 (MQ=255)

                                      cacaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCa                                                               >  1:1777299/1‑40 (MQ=255)

                                      cacaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCa                                                               >  1:3113715/1‑40 (MQ=255)

                                      cacaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCTGTTTATCATCGGTCAg                                <  1:2401686/71‑1 (MQ=255)

                                      cacaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAAt                                                        <  1:3863528/47‑1 (MQ=255)

                                       acaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGc                               <  1:1037731/71‑1 (MQ=255)

                                       acaAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGc                               <  1:1960282/71‑1 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:525336/1‑38 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:2867507/1‑38 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:1993283/1‑38 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:1468981/1‑38 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTat                                          >  1:1082060/1‑59 (MQ=255)

                                        caAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTat                                          >  1:1231934/1‑59 (MQ=255)

                                          aaCGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGtt                            <  1:3939371/71‑1 (MQ=255)

                                          aaCGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGtt                            <  1:3181069/71‑1 (MQ=255)

                                          aaCGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:3864948/1‑36 (MQ=255)

                                          aaCGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCa                                                               >  1:407252/1‑36 (MQ=255)

                                            cGTGTGG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGc                          <  1:16920/71‑1 (MQ=255)

                                            cGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGt                             >  1:2089670/1‑68 (MQ=255)

                                            cGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGc                          <  1:558418/71‑1 (MQ=255)

                                            cGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGc                          <  1:4119650/71‑1 (MQ=255)

                                               gtgG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAg                                <  1:846977/62‑1 (MQ=255)

                                                tgG‑‑‑CATCATCCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCag                       >  1:3747608/1‑70 (MQ=255)

                                                tgG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCag                       <  1:2824779/70‑1 (MQ=255)

                                                tgG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCag                       <  1:3493418/70‑1 (MQ=255)

                                                tgG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCag                       <  1:2016858/70‑1 (MQ=255)

                                                 gg‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCg                              >  1:3376827/1‑62 (MQ=255)

                                                          atcCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTat                                          >  1:3980609/1‑44 (MQ=255)

                                                          atcCTTTTGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTa                                           >  1:1633822/1‑43 (MQ=255)

                                                          atcCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCa                >  1:1446626/1‑70 (MQ=255)

                                                          atcCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCAt               >  1:346909/1‑71 (MQ=255)

                                                          atcCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCAt               >  1:4018028/1‑71 (MQ=255)

                                                             cTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTc                                  >  1:1205675/1‑49 (MQ=255)

                                                             cTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTc                                  >  1:93487/1‑49 (MQ=255)

                                                             cTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTc                                  >  1:1018840/1‑49 (MQ=255)

                                                              cttttGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTc                                  >  1:3563708/2‑48 (MQ=255)

                                                               tttGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTatca                                        >  1:2622941/1‑41 (MQ=255)

                                                               tttGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCgg                                    >  1:1114879/1‑45 (MQ=255)

                                                                 tGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGc        >  1:2998286/1‑71 (MQ=255)

                                                                 tGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGc        >  1:1916663/1‑71 (MQ=255)

                                                                 tGGCTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGc        >  1:2220645/1‑71 (MQ=255)

                                                                 tGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTg         <  1:183062/70‑1 (MQ=255)

                                                                 tGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTg         <  1:2442516/70‑1 (MQ=255)

                                                                    cTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     <  1:1404954/71‑1 (MQ=255)

                                                                    cTAGTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     <  1:2501599/71‑1 (MQ=255)

                                                                    cTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     <  1:2446164/71‑1 (MQ=255)

                                                                     tAATCGGCTGCAGTGCAATGACTCGCGGTTTATCTTCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     >  1:3623557/1‑70 (MQ=255)

                                                                     tAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     >  1:1384408/1‑70 (MQ=255)

                                                                     tAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTc     >  1:3883144/1‑70 (MQ=255)

                                                                       aTCGTCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTCAat  <  1:3149356/71‑1 (MQ=255)

                                                                       aTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTTCTTCaa   <  1:882217/70‑1 (MQ=255)

                                                                       aTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCttaat   <  1:1051201/70‑4 (MQ=255)

                                                                       aTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTCaa   <  1:3952820/70‑1 (MQ=255)

                                                                       aTCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTCAat  <  1:3829605/71‑1 (MQ=255)

TCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGG‑‑‑CATCATCCTTTTGGCTAATCGGCTGCAGTGCAATGACTCGCGGTTTATCATCGGTCAGCGTTGCCAGTAGTTCATCCAGTGCTTCAAT  >  minE/1874261‑1874399

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: `‑`

GATK/CNVnator alignment

N/A