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	1,868,106	G→A	35.0%	D265D (GAC→GAT)	ygcU ←	predicted FAD containing dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,868,106	0	G	A	35.0%	70.5 / 51.7	94	D265D (GAC→GAT)	ygcU	predicted FAD containing dehydrogenase
Reads supporting (aligned to +/- strand): ref base G (19/42); new base A (15/18); total (34/60)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAA  >  minE/1868047‑1868168

aaGATCAGCACGCTTTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACaa                                                        >  1:1304997/1‑68 (MQ=255)

aaGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACaa                                                        >  1:996027/1‑68 (MQ=255)

aaGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACaa                                                        >  1:1648400/1‑68 (MQ=255)

aaGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACaa                                                        >  1:2309456/1‑68 (MQ=255)

aaGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACaa                                                        >  1:1041845/1‑68 (MQ=255)

  gATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACg                                                     <  1:2655580/69‑1 (MQ=255)

  gATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACg                                                     <  1:1602330/69‑1 (MQ=255)

  gATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACg                                                     <  1:2148352/69‑1 (MQ=255)

   aTCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACg                                                     <  1:781782/68‑1 (MQ=255)

     cAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGc                                                  <  1:1110001/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCTAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:2341394/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:1113053/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:549324/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:3430558/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:1861492/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:886414/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:3135438/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:1169390/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCg                                                 <  1:2598264/69‑1 (MQ=255)

      aGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGGCATACAAACGAGCg                                                 <  1:1068662/69‑1 (MQ=255)

                ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATTCAAACGAGCGATTgacggac                                       >  1:3293625/1‑69 (MQ=255)

                ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                       <  1:2030593/69‑1 (MQ=255)

                ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                       >  1:3269741/1‑69 (MQ=255)

                ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                       >  1:129776/1‑69 (MQ=255)

                ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                       <  1:1791895/69‑1 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGcatcat                                                            >  1:1727114/1‑43 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATAc                                  <  1:808494/69‑1 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACa                                                         >  1:1545746/1‑46 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGAt                                    >  1:1667815/1‑67 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATa                                   >  1:3400975/1‑68 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATa                                   >  1:64794/1‑68 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                  >  1:1724484/1‑69 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                  >  1:1435777/1‑69 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                  >  1:3334906/1‑69 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                  >  1:288316/1‑69 (MQ=255)

                     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                  >  1:2633777/1‑69 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:1756132/1‑68 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:2039051/1‑68 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:849025/1‑68 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:1755929/1‑68 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:2660618/1‑68 (MQ=255)

                            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                            >  1:2181702/1‑68 (MQ=255)

                               gggTGAAGTGTTGTGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:190496/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACg                                                     <  1:334349/40‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1163617/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:2496363/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1449635/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:940085/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:939438/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1141345/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:2720634/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:2766762/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:3238198/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1440234/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1657497/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1933360/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1879192/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:1859393/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:594872/56‑1 (MQ=255)

                               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:528403/56‑1 (MQ=255)

                                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                       <  1:3156726/69‑1 (MQ=255)

                                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                       <  1:3248891/69‑1 (MQ=255)

                                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                       <  1:1041147/69‑1 (MQ=255)

                                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                       <  1:258105/69‑1 (MQ=255)

                                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                       <  1:1733276/69‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:1025267/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:2740489/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:99338/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:864324/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:1399360/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:1666437/68‑1 (MQ=255)

                                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                  <  1:197698/68‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:2134115/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:2972676/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1268295/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:2076471/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1552123/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1724855/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:499281/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1556149/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:532619/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1569941/59‑1 (MQ=255)

                                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                      <  1:1612596/59‑1 (MQ=255)

                                                ccATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                     <  1:2007406/39‑1 (MQ=25)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACGATGATTTCACGCAGGATGTTGa   >  1:2097888/1‑68 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:1340929/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:1627341/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:1337979/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:2938566/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:2387373/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:536647/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:3419303/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:1908528/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:1912391/1‑69 (MQ=255)

                                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa  >  1:3264592/1‑69 (MQ=255)

AAGATCAGCACGCATTTTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAA  >  minE/1868047‑1868168

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