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	2,253,072	C→G	31.3%	A1322A (GCG→GCC)	rpoC ←	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,253,072	0	C	G	31.3%	93.3 / 52.8	67	A1322A (GCG→GCC)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand): ref base C (29/17); new base G (13/8); total (42/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCGGGAGTAAGTTG  >  minE/2253004‑2253139

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

cgcAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCcgc                                                                   <  1:3930343/71‑1 (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                                                >  1:4323849/1‑71 (MQ=255)

                   ccGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGtt                                                >  1:1041079/1‑71 (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                                                         <  1:4396902/42‑2 (MQ=255)

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

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

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

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

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

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

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

                                       aGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGa                             >  1:3678840/1‑70 (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                           <  1:3052781/71‑1 (MQ=255)

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

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

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

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

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

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

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

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

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

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

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

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

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

                                         cACGCGGGTGGTTTCCTGGAACGATGCGGCCGAGATGAACGa                                                       >  1:838693/1‑42 (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)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCtt                                   <  1:3973221/47‑1 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCt                                    >  1:2139130/1‑46 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGt                               >  1:877257/1‑51 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGt                               >  1:4074258/1‑51 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGt                               >  1:4051475/1‑51 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCgg            >  1:3199377/1‑70 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCgg            <  1:1870147/70‑1 (MQ=255)

                                                        cTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCgg            <  1:4253263/70‑1 (MQ=255)

                                                           gAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGAt                            >  1:3847572/1‑51 (MQ=255)

                                                           gAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGAt                            >  1:3636370/1‑51 (MQ=255)

                                                           gAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGAt                            >  1:1778829/1‑51 (MQ=255)

                                                           gAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGAt                            >  1:2321255/1‑51 (MQ=255)

                                                           gAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCGGGAg         >  1:1242992/1‑70 (MQ=255)

                                                             aCGCTGCCGCGGAGATGAAGGACTCGGTTGCCAgaga                                        >  1:2061427/1‑37 (MQ=255)

                                                             aCGATGCCGCGGAGATGAAGGACTCGGTTGCCaga                                          >  1:1988304/1‑35 (MQ=255)

                                                             aCGATGCCGCGGAGATGAAGGACTCGGTTGCCAgaga                                        >  1:5085138/1‑37 (MQ=255)

                                                             aCGATGCCGCGGAGATGAAGGACTCGGTTGCCAgaga                                        >  1:705834/1‑37 (MQ=255)

                                                             aCGATGCCGCGGAGATGAAGGACTCGGTTGCCAgaga                                        >  1:5100485/1‑37 (MQ=255)

                                                             aCGATGCCGCGGAGATGAAGGACTCGGTTGCCAgaga                                        >  1:4865944/1‑37 (MQ=255)

                                                                 tGCCGCGGAGATGAAGGACTCGGTTGCCAGAGATGCTTTGGTGATACCCAGCAGATCGCGGGAGTAAGTTg  <  1:2661028/71‑1 (MQ=255)

                                                                 tGCCGCGGAGATGAAGGACTCCGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCGGGAGTAAGTTg  <  1:408744/71‑1 (MQ=255)

CGCAGTTCGTCGCGTTTGCCCGCAACGGCTGCTTCGGTCAGCACGCGAGTGGTCTCCTGGAACGATGCCGCGGAGATGAAGGACTCGGTTGCCAGAGACGCTTTGGTGATACCCAGCAGATCGCGGGAGTAAGTTG  >  minE/2253004‑2253139

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