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	608,403	C→A	46.1%	T617T (ACG→ACT)	pflB ←	pyruvate formate lyase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	608,403	0	C	A	46.1%	25.2 / 80.1	78	T617T (ACG→ACT)	pflB	pyruvate formate lyase I
Reads supporting (aligned to +/- strand): ref base C (5/37); new base A (11/25); total (16/62)
Fisher's exact test for biased strand distribution p-value = 5.24e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.38e-01

TGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGT  >  minE/608341‑608464

tGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGAGCGTCTGGGGTGTTACCCGTTTTc                                                         <  1:3006509/69‑1 (MQ=255)

tGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTc                                                         <  1:2479977/69‑1 (MQ=255)

tGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTc                                                         <  1:1945221/69‑1 (MQ=255)

       ggTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                                                   >  1:1011433/1‑68 (MQ=255)

       ggTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                                                   >  1:2333460/1‑68 (MQ=255)

       ggTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCa                                                   >  1:2041849/1‑68 (MQ=255)

          tAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATac                                                >  1:2234463/1‑68 (MQ=255)

           aGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATacac                                              >  1:337553/1‑69 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:3112143/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1237855/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:391001/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2056675/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2189763/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2263962/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:229315/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:803572/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:706322/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2352984/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1031602/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2387780/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:290086/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2678386/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:286592/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2722315/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:2786403/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1695144/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1523963/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1536247/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:594335/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1706138/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:1713523/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:507534/69‑1 (MQ=255)

              aCCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCAGTTTTCTTACCATACACAAc                                           <  1:643053/69‑1 (MQ=255)

                    tCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGa                                     <  1:2566145/69‑1 (MQ=255)

                    tCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGa                                     <  1:1685117/69‑1 (MQ=255)

                    tCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGa                                     <  1:2599689/69‑1 (MQ=255)

                    tCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGa                                     <  1:153433/69‑1 (MQ=255)

                    tCCGAACGGCGCGCCAACACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGa                                     <  1:1649928/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:1487043/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:1860768/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:2552379/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:2520271/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:3288691/69‑1 (MQ=255)

                        aaCGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:1924178/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACTACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:3229640/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:2392112/67‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:579473/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:2570798/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:217632/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:1115507/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:2660490/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:1435188/69‑1 (MQ=255)

                          cGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:711268/69‑1 (MQ=255)

                                gcCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:1022478/69‑1 (MQ=255)

                                gcCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:668847/69‑1 (MQ=255)

                                gcCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:1583391/69‑1 (MQ=255)

                                 ccAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:233725/68‑1 (MQ=255)

                                 ccAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:1481238/68‑1 (MQ=255)

                                 ccAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAg                         <  1:383581/68‑1 (MQ=255)

                                   aGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:2813517/60‑1 (MQ=255)

                                        gacgacCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:1751071/53‑1 (MQ=255)

                                          cgacCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTg                                 <  1:2574991/51‑1 (MQ=255)

                                          cgacCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGa               <  1:3279719/69‑1 (MQ=255)

                                          cgacCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGa               <  1:1563723/69‑1 (MQ=255)

                                          cgacCGGCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGa               <  1:1092192/69‑1 (MQ=255)

                                                 cTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGa        <  1:716919/69‑1 (MQ=255)

                                                    gggTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGAt                               <  1:2136424/43‑1 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGAt                               >  1:231826/1‑40 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCg   >  1:2701985/1‑68 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCg   >  1:2190143/1‑68 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:1994528/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:3263904/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:1385680/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:1359181/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:1311187/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:3245535/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:2380770/1‑69 (MQ=255)

                                                       tgtTACCAGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGt  >  1:992828/1‑69 (MQ=255)

TGCATCGGGTTAGCACCCGGTCCGAACGGCGCGCCAGCACGACGACCGTCTGGGGTGTTACCCGTTTTCTTACCATACACAACGTTAGAAGTGATGGTCAGAACAGACTGAGTCGGGATAGCGT  >  minE/608341‑608464

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