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	1,967,397	C→T	61.2%	E411E (GAG→GAA)	tktA ←	transketolase 1, thiamin‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,967,397	0	C	T	61.2%	60.9 / 92.3	134	E411E (GAG→GAA)	tktA	transketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand): ref base C (24/28); new base T (12/70); total (36/98)
Fisher's exact test for biased strand distribution p-value = 1.08e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

Only 100 of 134 total aligned reads displayed.

GGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGAACCAG  >  minE/1967337‑1967458

ggTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAac                                                       >  1:2326937/1‑69 (MQ=255)

ggTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAac                                                       >  1:505274/1‑69 (MQ=255)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1060310/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:2072864/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:3017136/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:2029035/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:3303047/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1989937/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:384504/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1917442/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1768548/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:391417/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1684888/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:470258/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:2773791/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:541657/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:582793/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1303948/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:1569656/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:829233/68‑3 (MQ=21)

ggTATACGGCAGGAAACCACCGTGCAGGGAGATACCGTTGGCAATCGCAGTCATACCGAATTcacgta                                                        <  1:112568/68‑3 (MQ=21)

         cAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg                                              <  1:2166205/69‑1 (MQ=255)

         cAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg                                              <  1:2841440/69‑1 (MQ=255)

         cAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg                                              <  1:2107727/69‑1 (MQ=255)

          aGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg                                              <  1:268659/68‑1 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:3345326/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:2206112/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:2862896/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:2257766/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:3429054/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:794175/1‑67 (MQ=255)

             aaGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGa                                            >  1:1562746/1‑67 (MQ=255)

                 cACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTcgc                                                           >  1:1782405/1‑48 (MQ=255)

                 cACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGt                                      >  1:12259/1‑69 (MQ=255)

                 cACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGt                                      >  1:72237/1‑69 (MQ=255)

                            gagaTACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGCTACCCgcagca                           <  1:2408366/69‑1 (MQ=255)

                                 aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTa                                        <  1:3005394/51‑1 (MQ=255)

                                 aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTa                                        <  1:1546590/51‑1 (MQ=255)

                                 aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTc                      >  1:2911363/1‑69 (MQ=255)

                                 aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTc                      >  1:2915444/1‑69 (MQ=255)

                                 aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTc                      >  1:2299892/1‑69 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:504729/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:654429/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:904909/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:2645579/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:1667559/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:2213404/69‑1 (MQ=255)

                                  ccGTTGGCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg                     <  1:1450941/69‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2974079/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2132596/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2050818/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:3069125/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:3115126/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:138787/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:3161783/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:620063/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:3239033/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:150418/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:1529469/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:3306198/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:1580453/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:1934840/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:1607296/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2933495/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2434351/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2502785/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:242233/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2403978/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2674111/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:889411/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2276340/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2861292/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2204928/67‑1 (MQ=255)

                                      tggCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:2925403/67‑1 (MQ=255)

                                      tAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg                                              <  1:1269193/40‑1 (MQ=255)

                                       aGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 >  1:1991688/1‑68 (MQ=255)

                                        gCAATCGCAGTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGa                 <  1:1743370/67‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:2782938/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:2288146/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:1380083/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:3401730/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:3435291/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:1920946/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:2936998/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGt                                         <  1:2426652/38‑1 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGc             >  1:112058/1‑66 (MQ=255)

                                             cgcgGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGc             >  1:285532/1‑66 (MQ=255)

                                              gcgGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCttt          >  1:45477/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:1999312/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:3295299/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:5998/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:3217011/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:3130526/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:701577/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:3130017/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:2363493/1‑68 (MQ=255)

                                                 gTCATACCGAATTCACGTACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGa       >  1:2551578/1‑68 (MQ=255)

                                                  tCATACCGAACTCGCGAGCACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGAAc     <  1:3313506/69‑1 (MQ=255)

                                                      aCCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGAACCAg  <  1:2193299/68‑1 (MQ=255)

                                                      aCCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGAACCAg  <  1:836238/68‑1 (MQ=255)

GGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTGCTTTAGAACCAG  >  minE/1967337‑1967458

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