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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,098,989	A→G	H115R (CAC→CGC)	rhaR →	transcriptional activator of rhaSR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,098,989	0	A	G	100.0%	130.4 / NA	38	H115R (CAC→CGC)	rhaR	transcriptional activator of rhaSR
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/17); total (21/17)

TACATTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACACTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTGAATCGCCATCGTTA  >  NC_000913/4098844‑4099136

tACATTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGgc                                                                                                                                                >  2:278529/1‑151 (MQ=255)

tACATTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGgc                                                                                                                                                >  1:448577/1‑151 (MQ=255)

tACATTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGgc                                                                                                                                                >  1:338349/1‑151 (MQ=255)

   aTTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCGGGGCAACCACGCTGGCGCt                                                                                                                                             >  1:5435/1‑151 (MQ=255)

            gACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGc                                                                                                                                     >  1:237215/1‑150 (MQ=255)

                aTAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATggg                                                                                                                                >  2:464110/1‑151 (MQ=255)

                  aaaCACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATgggg                                                                                                                               >  2:353291/1‑150 (MQ=255)

                  aaaCACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATgggg                                                                                                                               >  2:472964/1‑150 (MQ=255)

                     cacTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATgg                                                                                                                           <  1:278529/151‑1 (MQ=255)

                      acTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGgc                                                                                                                          <  1:253167/151‑1 (MQ=255)

                                        aCGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTAt                                                                                                        <  2:348724/151‑1 (MQ=255)

                                           aTCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCgg                                                                                                     >  2:323177/1‑151 (MQ=255)

                                               ggTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCg                                                                                                      <  1:500841/146‑1 (MQ=255)

                                               ggTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTc                                                                                                   >  1:322614/1‑149 (MQ=255)

                                                ggtttGCAGAATATTATTTATTACCGGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGTCGATTCCGGGATTTAACGCCGGCGCAGGGCAACCACGGTGGCGCTTAGGTAGCATGGGGATGGCGCGGGCGCGGTAGGTTATCGGt                                                                                                    >  1:193572/3‑147 (MQ=255)

                                                       aGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGc                                                                                          >  2:104808/1‑150 (MQ=255)

                                                          atatTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATg                                                                                       >  2:95005/1‑150 (MQ=255)

                                                              tatttattGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAag                                                                                   <  1:409270/150‑1 (MQ=255)

                                                               atttattGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAagt                                                                                  >  2:532440/1‑150 (MQ=255)

                                                               atttattGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAagt                                                                                  <  1:28001/150‑1 (MQ=255)

                                                                 ttattGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAagtag                                                                                <  1:63651/150‑1 (MQ=255)

                                                                  tattGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTc                                                                              >  1:633425/1‑151 (MQ=255)

                                                                         cGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCAtgt                                                                       <  2:432389/151‑1 (MQ=255)

                                                                            aGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCTATTCCGGGATTTAACGCCAGCGCAGGGCAGCCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGcc                                                                    <  2:372555/151‑1 (MQ=255)

                                                                            aGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGcc                                                                    >  1:90144/1‑151 (MQ=255)

                                                                            aGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGcc                                                                    >  2:200547/1‑151 (MQ=255)

                                                                               gTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGtt                                                                 >  2:336180/1‑151 (MQ=255)

                                                                                    aaGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTa                                                            <  1:622480/151‑1 (MQ=255)

                                                                                      gCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAAc                                                          <  1:200546/151‑1 (MQ=255)

                                                                                           aTCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAAt                                                     >  2:256725/1‑151 (MQ=255)

                                                                                                          gggCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGtt                                      <  2:93697/151‑1 (MQ=255)

                                                                                                              gATTCCGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCggg                                  >  2:285088/1‑151 (MQ=255)

                                                                                                                  ccGGGATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGt                              <  2:448582/151‑1 (MQ=255)

                                                                                                                      gATTTAACGCCAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGt                          <  1:409944/151‑1 (MQ=255)

                                                                                                                                cAGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTg                <  1:507260/151‑1 (MQ=255)

                                                                                                                                 aGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCCTGGGGATGGCGCAGGCGCGGCAGGTTATCGGTGAGCTTGAGCATGAAAGCAGTCAGCATGTGCCGTTTGCTAACGAAACGGCTGAGTTGCTGCTCGGGCAGTAGGTGATGGTGCTg                >  1:328577/1‑150 (MQ=255)

                                                                                                                                 aGCGCAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTGa               <  1:527190/151‑1 (MQ=255)

                                                                                                                                     cAGGGCAACCACGCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTGAATCg           <  2:297748/151‑1 (MQ=255)

                                                                                                                                              cacgCTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTGAATCGCCATCGTTa  <  1:180748/151‑1 (MQ=255)

TACATTCATGCTGACGATAAACACTCCTACGCTTCCGTTAACGATCTGGTTTTGCAGAATATTATTTATTGCCCGGAGCGTCTGAAGCTGAATCTTGACTGGCAGGGGGCGATTCCGGGATTTAACGCCAGCGCAGGGCAACCACACTGGCGCTTAGGTAGCATGGGGATGGCGCAGGCGCGGCAGGTTATCGGTCAGCTTGAGCATGAAAGTAGTCAGCATGTGCCGTTTGCTAACGAAATGGCTGAGTTGCTGTTCGGGCAGTTGGTGATGTTGCTGAATCGCCATCGTTA  >  NC_000913/4098844‑4099136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A