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	1,223,717	G→A	31.7%	T764T (ACG→ACA)	yebT →	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,223,717	0	G	A	31.7%	76.6 / 44.5	88	T764T (ACG→ACA)	yebT	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (35/25); new base A (5/23); total (40/48)
Fisher's exact test for biased strand distribution p-value = 4.77e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACATTG  >  minE/1223661‑1223777

gATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGTATCGGTACACCTGTGCTGtt                                                   >  1:164165/1‑68 (MQ=255)

gATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGTATCGGTACACCTGTGCTGTTc                                                  >  1:2351356/1‑69 (MQ=255)

gATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGTATCGGTACACCTGTGCTGTTc                                                  >  1:1912703/1‑69 (MQ=255)

gATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGTATCGGTACACCTGTGCTGTTc                                                  >  1:1816926/1‑69 (MQ=255)

gATGGCTTAAGCATTATTGTTGAAGCGCAGGAAGCCGGTTCGTTAGGTATCGGTACACCTGTGCTGTTc                                                  >  1:1845780/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:514273/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:644866/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:2823192/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:835511/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:2349916/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:2318052/1‑69 (MQ=255)

             ttattGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAg                                     >  1:1888213/1‑69 (MQ=255)

                ttgttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTc                                   >  1:984989/1‑68 (MQ=255)

                ttgttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTc                                   >  1:2836705/1‑68 (MQ=255)

                ttgttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTc                                   >  1:2368327/1‑68 (MQ=255)

                ttgttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTc                                   >  1:149028/1‑68 (MQ=255)

                  gttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCgg                                 <  1:2565510/68‑1 (MQ=255)

                  gttgAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCgg                                 <  1:879413/68‑1 (MQ=255)

                        gcgcCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGt                           <  1:1153866/68‑1 (MQ=255)

                        gcgcCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGt                           <  1:100508/68‑1 (MQ=255)

                        gcgcCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGt                           <  1:1904961/68‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:454360/69‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3358363/69‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3313818/69‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3277224/69‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:2857966/69‑1 (MQ=255)

                             ggAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:1698650/69‑1 (MQ=255)

                              gAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGa                    >  1:681318/1‑69 (MQ=255)

                              gAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGa                    >  1:1196839/1‑69 (MQ=255)

                              gAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGa                    >  1:2317154/1‑69 (MQ=255)

                              gAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGa                    >  1:3138117/1‑69 (MQ=255)

                              gAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGa                    >  1:1301792/1‑69 (MQ=255)

                                       tCGTTATGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:2523441/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3152195/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:1503705/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:2858574/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3146254/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:1479220/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3245632/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3249566/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3278231/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:3281935/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:593620/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:2440360/59‑1 (MQ=255)

                                       tCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAgg                     <  1:1287431/59‑1 (MQ=255)

                                               taTCGGTACACC‑‑TGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1102040/67‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTTGGGACATTg  <  1:1734880/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:2600058/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:952368/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:576507/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:375848/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1460746/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:3351700/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1436712/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:157060/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1954146/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:904594/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1595776/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:3235961/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:959639/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1242030/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:3100677/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:3046852/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1681935/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:1176698/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:693512/69‑1 (MQ=255)

                                                aTCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTCACCGGAATGACGCTGGGGACATTg  <  1:3235882/69‑1 (MQ=255)

                                                 tCGGTACACCTGTGCTGTTCCGTGGTCTGGAAGTAGGTACGGTTACCGGAATGACGCTGGGGACATTg  <  1:2223916/68‑1 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACa     <  1:2899257/63‑1 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:865226/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:905328/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2620333/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:752833/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:439193/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:401686/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:353139/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:3419214/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:3344329/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2705109/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2605308/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2588500/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2267948/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:2173788/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:1781577/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:1561709/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:1559875/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:1374546/1‑65 (MQ=255)

                                                   ggTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACAtt   >  1:1035752/1‑65 (MQ=255)

GATGGCTTAAGCATTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACGCCTGTGCTGTTCCGTGGTCTGGAAGTCGGTACGGTTACAGGAATGACGCTGGGGACATTG  >  minE/1223661‑1223777

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