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	1,351,725	G→A	56.5%	intergenic (‑171/+202)	udk ← / ← thiD	uridine/cytidine kinase/bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,351,725	0	G	A	56.5%	13.2 / 47.3	62	intergenic (‑171/+202)	udk/thiD	uridine/cytidine kinase/bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base G (10/17); new base A (10/25); total (20/42)
Fisher's exact test for biased strand distribution p-value = 5.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCTCAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCG  >  minE/1351664‑1351792

gcgcTCAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTa                                                              <  1:2102019/69‑1 (MQ=255)

   cTCAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaa                                                           <  1:1031107/69‑1 (MQ=255)

     caaagTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaaaa                                                         >  1:2623583/4‑69 (MQ=255)

     cAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaaaa                                                         >  1:2558186/1‑69 (MQ=255)

     cAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaaaa                                                         >  1:3363461/1‑69 (MQ=255)

     cAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaaaa                                                         >  1:307175/1‑69 (MQ=255)

     cAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTaaaaa                                                          >  1:2496181/1‑68 (MQ=255)

        agTTAATTGTTGACGAAGAATTCCCGGTGGCAAATTACGTTGATCAGTTTTATACAAGGTAAAAAAt                                                        <  1:2125475/67‑1 (MQ=255)

        agTTAATTGTTGACGAAGAATTCCCGGTGGCAAATTACGTTGATCAGTTTTATACAAGGTAAAAAAt                                                        <  1:1272431/67‑1 (MQ=255)

        agTTAATTGTTGACGAAGAATTCCCGGTGGCAAATTACGTTGATCAGTTTTATACAAGGTAAAAAAt                                                        <  1:236152/67‑1 (MQ=255)

        agTTAATTGTTGACGAAGAATTCCCGGTGGCAAATTACGTTGATCAGTTTTATACAAGGTAAAAAAt                                                        <  1:391261/67‑1 (MQ=255)

        agTTAATTGTTGACGAAGAATTCCCGGTGGCAAATTACGTTGATCAGTTTTATACAAGGTAAAAAAt                                                        <  1:3275499/67‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACg                                                <  1:1260035/68‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACg                                                <  1:2841575/68‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACg                                                <  1:3322240/68‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACg                                                <  1:134766/68‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACg                                                <  1:1313316/68‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGc                                               <  1:3376510/69‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGc                                               <  1:736783/69‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGc                                               <  1:801399/69‑1 (MQ=255)

               tgttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGc                                               <  1:2583132/69‑1 (MQ=255)

                gttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCa                                              <  1:2005666/69‑1 (MQ=255)

                gttgACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCa                                              <  1:415901/69‑1 (MQ=255)

                              cccGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTAt                                >  1:992971/1‑69 (MQ=255)

                              cccGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTAt                                >  1:1510944/1‑69 (MQ=255)

                              cccGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTAt                                >  1:550515/1‑69 (MQ=255)

                              cccGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTAt                                >  1:2639678/1‑69 (MQ=255)

                              cccGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTAt                                >  1:862386/1‑69 (MQ=255)

                                cGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATc                               <  1:2293708/68‑1 (MQ=255)

                                cGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATc                               <  1:2872740/68‑1 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAATGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:1942125/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTgc                                         >  1:690793/1‑48 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:1650175/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:728933/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:2563107/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:2618292/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:683351/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:1669465/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:2238470/1‑69 (MQ=255)

                                          ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                    >  1:2084203/1‑69 (MQ=255)

                                               ttGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACtt               <  1:1806122/69‑1 (MQ=255)

                                               ttGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACtt               <  1:1802161/69‑1 (MQ=255)

                                                 gATCAGTTTTATACAATGTAAAAAATGTT‑‑ACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:332453/69‑1 (MQ=255)

                                                   tCAGTTTTATACAAGGT‑AAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:839616/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:3164327/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:3398032/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:598078/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1543006/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1316168/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1558979/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:3259325/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:3187126/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:31327/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:31028/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:2741162/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1848819/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1006854/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1943861/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:1948489/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:2351702/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:2247403/68‑1 (MQ=255)

                                                    cAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATg           <  1:2108722/68‑1 (MQ=255)

                                                             gTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCg  <  1:3296827/68‑1 (MQ=255)

                                                             gTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCg  <  1:1186246/68‑1 (MQ=255)

GCGCTCAGAGTTAATTGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCG  >  minE/1351664‑1351792

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