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	2,057,310	G→A	35.6%	T45T (ACG→ACA)	ttdA →	L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,057,310	0	G	A	35.6%	37.0 / 30.1	56	T45T (ACG→ACA)	ttdA	L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand): ref base G (8/28); new base A (12/8); total (20/36)
Fisher's exact test for biased strand distribution p-value = 8.20e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.81e-01

GATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTG  >  minE/2057247‑2057368

gATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACgtcgtc                                                       <  1:1065132/69‑1 (MQ=255)

  tttCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     >  1:2759009/1‑69 (MQ=255)

         ccGTATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:3265024/62‑1 (MQ=255)

         ccGAATGCCTGATGACGTGGTGTATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:2357833/62‑1 (MQ=255)

         ccGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:3247832/62‑1 (MQ=255)

         ccGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:2584717/62‑1 (MQ=255)

         ccGAATGCCCGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:2664474/62‑1 (MQ=255)

          cGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:945990/61‑1 (MQ=255)

          cGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGa                                                     <  1:2900060/61‑1 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGAt                            >  1:2176399/1‑68 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           <  1:1078419/69‑1 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:3339071/1‑69 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           <  1:3313533/69‑1 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:2681250/1‑69 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:2678908/1‑69 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:2133974/1‑69 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:1971809/1‑69 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           <  1:2002868/69‑1 (MQ=255)

                            gtggATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATg                           >  1:1112123/1‑69 (MQ=255)

                                  aaaCTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTc                        <  1:2186976/66‑1 (MQ=255)

                                  aaaCTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTc                        <  1:2646539/66‑1 (MQ=255)

                                  aaaCTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTc                        <  1:1729130/66‑1 (MQ=255)

                                      tAAAACAGCTAATGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:145860/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGtt                         >  1:2314110/1‑61 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:448849/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:3385945/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:1192590/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:619726/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:3243969/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:2932323/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:2715345/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:2704720/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:701881/1‑62 (MQ=255)

                                      tAAAACAGCTAAAGGATGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTc                        >  1:2350392/1‑62 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACGACATGCAAAAAGCGa     <  1:2295570/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:3171202/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:2137091/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:2210459/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:2263454/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:1750540/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:3169532/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:1945227/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:163602/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:676031/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:2739394/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:923352/68‑1 (MQ=255)

                                                   ggATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:753770/68‑1 (MQ=255)

                                                    gATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:3374817/67‑1 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:457099/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:986892/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:1235983/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:1381529/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:1892023/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:193624/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:2531897/69‑3 (MQ=255)

                                                     aTGCCGAAACATCGTCGATGGGAAAAATCATCTACCACACGATGTTCGATAACATGCAAAAAGCGAtcg  <  1:2292540/69‑3 (MQ=255)

                                                         cGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:2564279/62‑1 (MQ=255)

                                                               gtcgtcGATGGGGATAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa     <  1:1649993/56‑1 (MQ=255)

GATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTG  >  minE/2057247‑2057368

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A