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	2,078,091	G→A	47.3%	N142N (AAC→AAT)	uxaA ←	altronate hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,078,091	0	G	A	47.3%	6.6 / 62.1	74	N142N (AAC→AAT)	uxaA	altronate hydrolase
Reads supporting (aligned to +/- strand): ref base G (11/28); new base A (5/30); total (16/58)
Fisher's exact test for biased strand distribution p-value = 1.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGTGGCTGAAGAGGAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTAC  >  minE/2078028‑2078155

ggTGTGGCTGAAGAGGAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTg                                                             >  1:2567235/1‑69 (MQ=255)

  tgtgGCTGAAGAGGAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTgg                                                            <  1:2947421/68‑1 (MQ=255)

   gtgGCTGAAGAGGAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTgg                                                            <  1:709345/67‑1 (MQ=255)

              ggAACACGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGa                                               >  1:2084722/1‑69 (MQ=255)

              ggAACACGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGa                                               >  1:1852938/1‑69 (MQ=255)

              ggAACACGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGa                                               >  1:3329225/1‑69 (MQ=255)

              ggAACACGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGa                                               >  1:3159527/1‑69 (MQ=255)

              ggAACACGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGa                                               >  1:1685572/1‑69 (MQ=255)

               gAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTgg                                                            <  1:1841839/55‑1 (MQ=255)

                 acacGCGGTCTGTACCTTCAGCGTTGTTGGTCTCTTTCTGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:3044091/69‑1 (MQ=255)

                 acacGCCGTCGGTGCCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:1798262/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:248017/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:2067543/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:2737380/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:2901926/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:1862837/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:1727676/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:2997281/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:3058572/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:1422785/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:728283/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:818916/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:867023/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:1039965/69‑1 (MQ=255)

                 acacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTCGATCTGCCGCGCGATGc                                            <  1:180504/69‑1 (MQ=255)

                  cacGCCGTCGGTACCTTCAGCGTTGTTGGTCTCTTTCAGGAAACGATTTTGGATCTGCCGCGCGATGc                                            <  1:604527/68‑1 (MQ=255)

                  cacGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGcc                                           >  1:3428281/1‑69 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTg                                                       >  1:955038/1‑54 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCg                                          >  1:998354/1‑67 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGtt                                        >  1:1506129/1‑69 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGtt                                        >  1:1663247/1‑69 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGt                                         >  1:846910/1‑68 (MQ=255)

                     gCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGt                                         >  1:1911962/1‑68 (MQ=255)

                       cGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGa                                      <  1:1505307/69‑1 (MQ=255)

                       cGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGa                                      <  1:2281934/69‑1 (MQ=255)

                       cGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGa                                      <  1:3360240/69‑1 (MQ=255)

                       cGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGa                                      <  1:835379/69‑1 (MQ=255)

                           aGTACGTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:278673/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:274742/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:2696541/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:407657/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:2612671/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:3164099/54‑1 (MQ=255)

                           aGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:1114633/54‑1 (MQ=255)

                           aGTACCTTCGGCGTT‑TTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCcgcgc                                                 <  1:759826/53‑1 (MQ=255)

                               ccTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGccc                              >  1:1162840/1‑69 (MQ=255)

                               ccTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGccc                              >  1:3149105/1‑69 (MQ=255)

                               ccTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGccc                              >  1:939995/1‑69 (MQ=255)

                                       gttgttGGTCTCTTTCAGAAAACGGTGCTGGATCTGCCGCGCGATGCCGTTGa                                      <  1:610352/53‑1 (MQ=255)

                                        ttgttgGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGc                     <  1:225874/69‑1 (MQ=255)

                                            tgGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAgg                  <  1:1641539/68‑1 (MQ=255)

                                            tgGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAgg                  <  1:1778056/68‑1 (MQ=255)

                                                     tCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAg          <  1:3188625/67‑1 (MQ=255)

                                                     tCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAg          <  1:1717310/67‑1 (MQ=255)

                                                     tCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAg          <  1:449716/67‑1 (MQ=255)

                                                     tCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAg          <  1:1425472/67‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:1220806/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:214144/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:2440679/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:905474/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:2088736/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:207754/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:1920176/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:119207/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:744904/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:3312109/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:1295242/68‑1 (MQ=255)

                                                         gaaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:420382/68‑1 (MQ=255)

                                                          aaaCGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTa   <  1:495460/69‑1 (MQ=255)

                                                          aaaCGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTa   <  1:1454175/69‑1 (MQ=255)

                                                          aaaCGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTa   <  1:10473/69‑1 (MQ=255)

                                                          aaaCGGTTCTGGATCTGCCCCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTa   <  1:335637/69‑1 (MQ=255)

                                                          aaaCGATTTTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCAtt    <  1:832701/68‑1 (MQ=255)

                                                           aaCGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTAc  <  1:2853003/69‑1 (MQ=255)

GGTGTGGCTGAAGAGGAACACGCCGTCAGTACCTTCGGCGTTGTTGGTCTCTTTCAGAAAACGGTTCTGGATCTGCCGCGCGATGCCGTTGACACAGCCCACGGTTGGCAGGATCCACAGCTCATTAC  >  minE/2078028‑2078155

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