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	2,869,908	T→C	51.3%	D531D (GAT→GAC)	rnr →	exoribonuclease R, RNase R

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,869,908	0	T	C	51.3%	2.1 / 70.6	80	D531D (GAT→GAC)	rnr	exoribonuclease R, RNase R
Reads supporting (aligned to +/- strand): ref base T (23/16); new base C (27/14); total (50/30)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-01

CGGTAACAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGAA  >  minE/2869845‑2869968

cGGTAACAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGa                                                         <  1:1098294/69‑1 (MQ=255)

cGGTAACAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGa                                                         <  1:527836/69‑1 (MQ=255)

cGGTAACAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGa                                                         <  1:1569827/69‑1 (MQ=255)

     aCAAGCCGTAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAAtgc                                                    >  1:1912181/1‑69 (MQ=255)

     aCAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAAtgc                                                    >  1:2391769/1‑69 (MQ=255)

     aCAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAAtg                                                     >  1:1376974/1‑68 (MQ=255)

     aCAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAAtg                                                     >  1:2813924/1‑68 (MQ=255)

     aCAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCT‑ATGCAGAAAtgc                                                    >  1:3307698/1‑68 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:1811770/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:976339/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:1931885/69‑1 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:2022043/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:2086992/69‑1 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:2414707/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:260109/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:2783095/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:3182847/69‑1 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:739809/69‑1 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:1096453/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:152123/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             >  1:1548988/1‑69 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:1529109/69‑1 (MQ=255)

            ggAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCATGATGCAGAAATGCTGCAAAc                                             <  1:2976425/69‑1 (MQ=255)

             gAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:3128916/68‑1 (MQ=255)

             gAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:713671/68‑1 (MQ=255)

                ccGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCAtg                                         >  1:2952294/1‑69 (MQ=255)

                ccGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCAtg                                         >  1:158794/1‑69 (MQ=255)

                ccGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCAtg                                         >  1:585100/1‑69 (MQ=255)

                                aGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAAc                                             <  1:488842/49‑1 (MQ=255)

                                aGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGa                         <  1:1770704/69‑1 (MQ=255)

                                aGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGa                         <  1:1348934/69‑1 (MQ=255)

                                aGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGa                         <  1:1991838/69‑1 (MQ=255)

                                          gTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCg                 <  1:1472306/67‑1 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:555200/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1221385/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:71240/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:3368071/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1308716/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:3197586/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:730785/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:732646/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:3121745/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1219323/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1137995/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2895805/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1408659/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2753319/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2655907/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1908050/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2604851/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1476130/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2595625/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:150032/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:214256/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:1985678/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:2039253/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:210165/1‑43 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgct                                       >  1:3362732/1‑42 (MQ=255)

                                             ggTTGCCGATCGTCCTGACGCAGAAAAGCTGCAAACCAtgctg                                      >  1:2909961/1‑43 (MQ=38)

                                             ggTTACCGATCGTCCTGACGCAGAAATGCTGCAAACCAtgctg                                      >  1:488948/1‑43 (MQ=38)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:448143/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:1866208/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:598123/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:1998089/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:1944196/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:1656410/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:3359141/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:331715/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:2255924/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:233215/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:3158931/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:2400006/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:2503121/69‑1 (MQ=255)

                                                tGCCGATCGTCCTGACGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGa         <  1:2756810/69‑1 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCg                 >  1:2278747/1‑54 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGaa  >  1:441771/1‑69 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGaa  >  1:1998862/1‑69 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGaa  >  1:710030/1‑69 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGaa  >  1:2655351/1‑69 (MQ=255)

                                                       cGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGa   >  1:211166/1‑68 (MQ=255)

CGGTAACAAGCCGGAACCGCGTGACTACGCGGAGCTGCTGGAGTCGGTTGCCGATCGTCCTGATGCAGAAATGCTGCAAACCATGCTGCTGCGCTCGATGAAACAGGCGATTTACGATCCAGAA  >  minE/2869845‑2869968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A