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	853,846	G→A	29.2%	Y111Y (TAC→TAT)	yciE ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	853,846	0	G	A	29.2%	57.5 / 23.2	58	Y111Y (TAC→TAT)	yciE	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (11/30); new base A (10/7); total (21/37)
Fisher's exact test for biased strand distribution p-value = 3.47e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

ATCGCTTCGATGGTTGGAATTGAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAG  >  minE/853781‑853910

aTCGCTTCGATGGTTGGAATTGAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTa                                                                <  1:1672889/68‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2900052/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2239260/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2507398/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2019929/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2600405/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:1584494/69‑1 (MQ=255)

                     gAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAAGAGTGAGGTATAACAGGCGATTTCAAATTGCTCg                                          <  1:2993670/69‑1 (MQ=255)

                         cTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGa                                      <  1:2760368/69‑1 (MQ=255)

                         cTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGa                                      <  1:2654387/69‑1 (MQ=255)

                         cTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGa                                      <  1:786042/69‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:29113/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:3167442/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:11809/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:2869861/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:3347747/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:689190/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:2535604/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:2331079/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:796237/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:2149371/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:2147950/49‑1 (MQ=255)

                                aCCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCa                                                   <  1:1212730/49‑1 (MQ=255)

                                   ggCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCt                            <  1:240417/69‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:2208417/68‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:1813943/68‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:849063/68‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:3250865/68‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:2466049/68‑1 (MQ=255)

                                                   gctAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGAc             <  1:2625625/68‑1 (MQ=255)

                                                    ctAATAGTGAGGTGTTACAGGCGATTTCAAATTGCTCGAAGACATATCCTCTAATAGAGCCTTTGAc             <  1:1389485/67‑1 (MQ=255)

                                                      aaTAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTAt          <  1:598796/68‑1 (MQ=255)

                                                       aTAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTAttt        >  1:699513/1‑69 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGAc                                     >  1:1945522/1‑37 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:791438/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:2189499/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:1248540/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:926025/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:2829477/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:2214310/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:2310188/1‑38 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtc       >  1:1681501/1‑67 (MQ=255)

                                                          gTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtc       >  1:577147/1‑67 (MQ=255)

                                                             aGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAg  <  1:221335/69‑1 (MQ=255)

                                                             aGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAg  <  1:1760681/69‑1 (MQ=255)

                                                             aGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAg  <  1:1245478/69‑1 (MQ=255)

                                                             aGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAg  <  1:2845117/69‑1 (MQ=255)

                                                             aGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAg  <  1:2114892/69‑1 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGCCATATCCGCTAATAGAGCCTTTGACTATTtcat     >  1:641010/1‑66 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACa                                    >  1:2641665/1‑35 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:2551532/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:877036/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:1040551/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:1196285/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:2069004/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:3413324/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:1625576/1‑67 (MQ=255)

                                                             aGGTATAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTtcatc    >  1:1697336/1‑67 (MQ=255)

ATCGCTTCGATGGTTGGAATTGAAGCTGTATCACCGGCATTTTTTGCTGCTGCTAATAGTGAGGTGTAACAGGCGATTTCAAATTGCTCGAAGACATATCCGCTAATAGAGCCTTTGACTATTTCATCAG  >  minE/853781‑853910

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