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	1,351,743	A→T	38.7%	intergenic (‑189/+184)	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	1,351,743	0	A	T	38.7%	48.5 / 68.1	76	intergenic (‑189/+184)	udk/thiD	uridine/cytidine kinase/bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base A (16/30); new base T (10/19); total (26/50)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

TGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATAAAATGTAAA  >  minE/1351679‑1351807

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                           ttACGTTGATCAGTTTTATACAAGGTAAAAAATGTTATACGCAGTTGCGCAAATTATCCGCCTTTACGt                                   >  1:1650175/1‑69 (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                          <  1:598078/68‑1 (MQ=255)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTa                                      >  1:1834823/1‑46 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGc                >  1:2975444/1‑68 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGc                >  1:2528368/1‑68 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:2684614/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:1251523/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:2082192/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:2952072/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:2930569/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:511133/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:1583010/1‑69 (MQ=255)

                                               tAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCa               >  1:149415/1‑69 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:2610277/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:2123507/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:798241/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:1526119/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:2144403/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:202306/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:676128/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:2895698/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:515261/69‑1 (MQ=255)

                                                      aaaaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:3014251/69‑1 (MQ=255)

                                                        aaaTGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATaaaa        <  1:2786008/67‑1 (MQ=255)

                                                            gTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATAAAATGTaaa  <  1:1661807/69‑1 (MQ=255)

                                                            gTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATAAAATGTaaa  <  1:3268106/69‑1 (MQ=255)

TGTTGACAAAGAATTCCCGGGGGCAAATTACGTTGATCAGTTTTATGTAAGGTAAAAAATGTTAAACGCAGTTGCGCAAATTATCCGCCTTTACGTCACTTTATGAGCAATTCGCATATAAAATGTAAA  >  minE/1351679‑1351807

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