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	2,975,229	G→A	57.9%	T528T (ACC→ACT)	yjjK ←	fused predicted transporter subunits and ATP‑binding components of ABC superfamily

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,975,229	0	G	A	57.9%	14.3 / 41.5	57	T528T (ACC→ACT)	yjjK	fused predicted transporter subunits and ATP‑binding components of ABC superfamily
Reads supporting (aligned to +/- strand): ref base G (5/19); new base A (10/23); total (15/42)
Fisher's exact test for biased strand distribution p-value = 5.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAGAATGTGCGT  >  minE/2975171‑2975288

tACGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGtt                                                     <  1:569042/67‑1 (MQ=255)

tACGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGtt                                                     <  1:1718419/67‑1 (MQ=255)

tACGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGtt                                                     <  1:2755348/67‑1 (MQ=255)

 aCGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTAcc                                                  <  1:980116/69‑1 (MQ=255)

 aCGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTAcc                                                  <  1:628127/69‑1 (MQ=255)

 aCGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTAcc                                                  <  1:3297240/69‑1 (MQ=255)

 aCGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTAcc                                                  <  1:1969342/69‑1 (MQ=255)

 aCGCTGCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTAcc                                                  <  1:564653/69‑1 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCTAAGAACTCAACtt                                 >  1:2540419/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:1119104/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:625001/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:3252077/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:2902657/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:2785012/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:2089207/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:1040369/1‑69 (MQ=255)

                  cgTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:1407391/1‑69 (MQ=255)

                  cgTCTGCGCCAAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACtt                                 >  1:583184/1‑69 (MQ=255)

                    tCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACttt                                <  1:2356583/68‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:953615/66‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:1145773/66‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:2974936/66‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:2017177/66‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:2050011/66‑1 (MQ=255)

                          cccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:3097896/66‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:1500096/65‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:3179232/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2095358/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:3070909/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:1169962/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2893618/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2178887/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2802717/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2780776/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2318492/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2352771/69‑1 (MQ=255)

                           ccAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2325534/69‑1 (MQ=255)

                            cAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:75593/68‑1 (MQ=255)

                            cAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:1980899/68‑1 (MQ=255)

                            cAGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2322998/68‑1 (MQ=255)

                             aGCGTGCGTTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCAt                        <  1:2127311/67‑1 (MQ=255)

                                   cgtTTCTTGTACTCTTCGTACTCAGTAAAGTTACCTTCGAAGAACTCAACTTTACCt                            <  1:3229158/57‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:2842981/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:824970/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:2250526/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:538988/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:424440/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:264299/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:292097/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:1631327/69‑1 (MQ=255)

                                     tttCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATc              <  1:2846870/69‑1 (MQ=255)

                                         ttGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAg           <  1:337782/68‑1 (MQ=255)

                                                ctTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACt                                  >  1:1479931/1‑38 (MQ=255)

                                                ctTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAg           >  1:3424304/1‑61 (MQ=255)

                                                ctTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAGAATGTGCg   >  1:2625492/1‑69 (MQ=255)

                                                ctTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAGAATGTGCg   >  1:2842309/1‑69 (MQ=255)

                                                 ttCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAGAATGTGCGt  >  1:1409076/1‑69 (MQ=255)

TACGCTTCGGCTCCAGCGCGTCTGCGCCCAGCGTGCGTTTCTTGTACTCTTCGTACTCGGTAAAGTTACCTTCGAAGAACTCAACTTTACCTTCATCCTGGTAATCCAGAATGTGCGT  >  minE/2975171‑2975288

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