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
A6 F1 I0 R2	251	90.0	5200563	86.9%	4519289	59.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,253,057	C→T	37.9%	E1327E (GAG→GAA)	rpoC ←	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,253,057	0	C	T	37.9%	44.3 / 55.3	56	E1327E (GAG→GAA)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand): ref base C (13/21); new base T (13/8); total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCTCTTTCAGGCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGC  >  minE/2252988‑2253127

gTTCTCTTTCAGACCACGCAGGAAGTCGCGCTTGCCGGTGACCGCCGCCTCGGTGAGGACGCGGGTGGtct                                                                       >  1:2904359/1‑71 (MQ=255)

gTTCTCTTTCAGACCACGCAGGAAGTCGCGCTTGCCGGTGACCGCCGCCTCGGTGAGGACGCGGGTGGtct                                                                       >  1:3086410/1‑71 (MQ=255)

gTTCTCTTTCAGACCACGCAGGAAGTCGCGCTTGCCGGTGACCGCCGCCTCGGTGAGGACGCGGGTGGtct                                                                       >  1:1357261/1‑71 (MQ=255)

gTTCTCTTTCAGACCACGCAGGAAGTCGCGCTTGCCGGTGACCGCCGCCTCGGTGAGGACGCGGGTGGtct                                                                       >  1:3843741/1‑71 (MQ=255)

     ctTTCAGGCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTg                                                                   >  1:118890/1‑70 (MQ=255)

     ctTTCAGGCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTg                                                                   >  1:4902793/1‑70 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:793870/71‑1 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:4869075/71‑1 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:3113567/71‑1 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:3488794/71‑1 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:1438947/71‑1 (MQ=255)

            gCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATg                                                           <  1:153693/71‑1 (MQ=255)

             ccGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGc                                                          <  1:99208/71‑1 (MQ=255)

                cgcAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCcgc                                                       <  1:3930343/71‑1 (MQ=255)

                cgcAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCcgc                                                       <  1:4151091/71‑1 (MQ=255)

                      tcgtcgCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGAt                                                 >  1:446644/1‑71 (MQ=255)

                        gtcgCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGa                                               <  1:3792987/71‑1 (MQ=255)

                        gtcgCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGa                                               <  1:4677691/71‑1 (MQ=255)

                                tggccGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTGTCCTGGAACGATGCCGCGGAGATGAAGGACTc                                        <  1:4065730/67‑1 (MQ=255)

                                 gCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCg                                       <  1:1987193/70‑1 (MQ=255)

                                   ccGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGtt                                    >  1:1041079/1‑71 (MQ=255)

                                   ccGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGtt                                    >  1:4323849/1‑71 (MQ=255)

                                    cGCAACGGCTGCTTCGGTCAGCACGCGAGTGGGCTCCTGGAACGATg                                                           <  1:3660481/47‑1 (MQ=255)

                                                 tCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCttt                      >  1:3491352/1‑71 (MQ=255)

                                                  cGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAggt                                           >  1:3801863/1‑48 (MQ=255)

                                                  cGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCtt                       <  1:1634887/69‑1 (MQ=255)

                                                   ggTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTgg                    <  1:1251468/71‑1 (MQ=255)

                                                    gTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGt                   >  1:2425062/1‑71 (MQ=255)

                                                       aGCACGGGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:2737307/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:1253965/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:1256645/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:4396902/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:4302292/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:1224086/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:2295718/42‑2 (MQ=255)

                                                       aGCACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGaac                                             <  1:2681639/42‑2 (MQ=255)

                                                       aGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGa                 >  1:3678840/1‑70 (MQ=255)

                                                       aGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGa                 >  1:2187203/1‑70 (MQ=255)

                                                       aGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGa                 >  1:4706076/1‑70 (MQ=255)

                                                       aGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAACGACTCGGTTGCCa                                >  1:2363949/1‑55 (MQ=255)

                                                        gCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:638836/71‑1 (MQ=255)

                                                        gCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:3874895/71‑1 (MQ=255)

                                                        gCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:845628/71‑1 (MQ=255)

                                                        gCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:1362392/71‑1 (MQ=255)

                                                        gCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:3052781/71‑1 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:838693/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:58809/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:4950113/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:860139/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:1059048/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:1504887/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:1985820/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:3801056/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:3768434/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:357429/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:2244842/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                           >  1:2832008/1‑42 (MQ=255)

                                                         cACGCGGGTGGTTTCCTGGAACGACGCGGCCGAGATGAACGa                                           >  1:4894285/1‑42 (MQ=16)

                                                         cACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATa               <  1:2065545/70‑1 (MQ=255)

                                                         cACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATAc              >  1:4366853/1‑71 (MQ=255)

                                                                     ctcCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATcgc  >  1:127303/1‑71 (MQ=255)

                                                                     ctcCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATcgc  >  1:1149570/1‑71 (MQ=255)

GTTCTCTTTCAGGCCGCGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGC  >  minE/2252988‑2253127

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A