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	1,914,848	T→C	27.0%	E208E (GAA→GAG)	ptsP ←	fused PEP‑protein phosphotransferase (enzyme I) of PTS system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,914,848	0	T	C	27.0%	55.7 / 24.8	37	E208E (GAA→GAG)	ptsP	fused PEP‑protein phosphotransferase (enzyme I) of PTS system
Reads supporting (aligned to +/- strand): ref base T (16/11); new base C (8/2); total (24/13)
Fisher's exact test for biased strand distribution p-value = 4.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.04e-01

GCGTTTGCTGTAGCGGCGAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTGC  >  minE/1914785‑1914914

gCGTTTGCTGTAGCGGCGAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCaga                                                              <  1:3906181/70‑1 (MQ=255)

         gTAGCGGCGAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCAGAGCCGGAt                                                       >  1:727762/1‑68 (MQ=255)

            gcggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGc                                                  >  1:1444942/1‑70 (MQ=255)

            gcggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCAGAGCCGGATCCAGc                                                  <  1:1967345/70‑1 (MQ=255)

              ggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCTAGCGtt                                               <  1:6364/71‑1 (MQ=255)

              ggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGtt                                               <  1:1179133/71‑1 (MQ=255)

              ggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGtt                                               <  1:2743590/71‑1 (MQ=255)

              ggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGtt                                               <  1:2549809/71‑1 (MQ=255)

              ggcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGtt                                               <  1:2533461/71‑1 (MQ=255)

               gcgAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGtt                                               <  1:3251780/70‑1 (MQ=255)

                 gAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGAt                                            >  1:1399678/1‑71 (MQ=255)

                 gAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGAt                                            >  1:3025403/1‑71 (MQ=255)

                     cTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAg                                                   <  1:901866/60‑1 (MQ=255)

                     cTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAg                                                   <  1:355716/60‑1 (MQ=255)

                     cTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAg                                                   <  1:225256/60‑1 (MQ=255)

                     cTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAg                                                   <  1:406677/60‑1 (MQ=255)

                     cTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCt                                        >  1:2199009/1‑71 (MQ=255)

                        gTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCAGAGcc                                                           >  1:2737540/1‑49 (MQ=255)

                        gTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCAGAGcc                                                           >  1:811077/1‑49 (MQ=255)

                           tGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGCTCCAGAGCCGGATCCAGCGTTGa                                             >  1:2913807/1‑60 (MQ=255)

                                      ccAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCAt                        >  1:3736465/1‑70 (MQ=255)

                                            ccccGGTCAGTCGTTCGCGCTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAgg                  >  1:3132152/1‑70 (MQ=255)

                                            ccccGGTCAGTCGTTCGCGCTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAgg                  >  1:3478122/1‑70 (MQ=255)

                                            ccccGGTCAGTCGTTCGCGCTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATGAAAgg                  >  1:3398566/1‑70 (MQ=255)

                                              ccGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTaa               >  1:2298805/1‑71 (MQ=255)

                                              ccGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTaa               <  1:483276/71‑1 (MQ=255)

                                                        gTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:982738/1‑71 (MQ=255)

                                                        gTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:3278135/1‑71 (MQ=255)

                                                        gTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:2074025/1‑71 (MQ=255)

                                                        gTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:1772263/1‑71 (MQ=255)

                                                        gTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:1605045/1‑71 (MQ=255)

                                                        gTTCGCGCTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATcc     >  1:3113956/1‑71 (MQ=255)

                                                           cgcgTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTg   >  1:2273967/1‑70 (MQ=255)

                                                           cgcgTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTg   >  1:1370299/1‑70 (MQ=255)

                                                           cgcgTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTg   >  1:1153198/1‑70 (MQ=255)

                                                           cgcgTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTGc  >  1:4096821/1‑71 (MQ=255)

                                                           cgcgTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTGc  >  1:1060233/1‑71 (MQ=255)

                                                               ttCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGc         <  1:3997325/60‑1 (MQ=255)

                                                               ttCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGc         <  1:1347089/60‑1 (MQ=255)

GCGTTTGCTGTAGCGGCGAAACTCGTTTGCCGCTTCTTCCAGCGCCCCGGTCAGTCGTTCGCGTTCCAGAGCCGGATCCAGCGTTGATGCCTGATACACCTGTTCCATTAAAGGTAACGTGGCATCCTGC  >  minE/1914785‑1914914

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