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 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,054,439	A→G	T280T (ACT→ACC)	glnG ←	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,054,439	0	A	G	100.0%	110.5 / NA	31	T280T (ACT→ACC)	glnG	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/15); total (16/15)

GCGCGCCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGAGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTTCGTCG  >  NC_000913/4054310‑4054565

gcgcgcCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCg                                                                                                                       <  2:927775/139‑1 (MQ=255)

 cgcgcCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGa                                                                                                                      >  1:999202/1‑139 (MQ=255)

 cgcgcCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGa                                                                                                                      >  2:331692/1‑139 (MQ=255)

          cGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGca                                                                                                             <  2:999202/139‑1 (MQ=255)

                             gTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGgcgc                                                                                          >  2:79378/1‑139 (MQ=255)

                               tCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCAt                                                                                        >  1:452817/1‑139 (MQ=255)

                                        ggcggcAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCaa                                                                               <  2:556268/139‑1 (MQ=255)

                                          cggcAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAAcg                                                                             <  2:452817/139‑1 (MQ=255)

                                                  gAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTaaaa                                                                     <  1:79378/139‑1 (MQ=255)

                                                         gATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCg                                                              >  1:703772/1‑139 (MQ=255)

                                                          aTAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGt                                                             >  1:921368/1‑139 (MQ=255)

                                                              cGTTCAGGCGGTGGAACAGATCTTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGgc                                                                                            <  1:597850/104‑1 (MQ=255)

                                                              cGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGgc                                                                                            >  2:597850/1‑104 (MQ=255)

                                                                     gCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCAcg                                                  <  2:921368/139‑1 (MQ=255)

                                                                                 aTCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGgtgggtgg                                                                                                                            >  1:893604/1‑53 (MQ=255)

                                                                                 aTCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGgtgggtgg                                                                                                                            <  2:893604/53‑1 (MQ=255)

                                                                                 aTCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATa                                                                                                                    <  1:213430/61‑1 (MQ=255)

                                                                                 aTCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATa                                                                                                                    >  2:213430/1‑61 (MQ=255)

                                                                                   ccTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATa                                                                                                                    >  2:305982/1‑59 (MQ=255)

                                                                                   ccTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATa                                                                                                                    <  1:305982/59‑1 (MQ=255)

                                                                                      cACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTg                                 >  1:347004/1‑139 (MQ=255)

                                                                                                aCCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGt                                                                                                                              <  1:901018/36‑1 (MQ=255)

                                                                                                       tGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCatat                >  1:261181/1‑139 (MQ=255)

                                                                                                         cACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCa              >  2:205267/1‑139 (MQ=255)

                                                                                                              gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAgccgcc                                                                                 >  1:686982/1‑67 (MQ=255)

                                                                                                              gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAgccgcc                                                                                 <  2:686982/67‑1 (MQ=255)

                                                                                                              gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAAt         >  1:729458/1‑139 (MQ=255)

                                                                                                              gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAAt         >  1:430717/1‑139 (MQ=255)

                                                                                                                    cGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcgtc   <  2:307464/139‑1 (MQ=255)

                                                                                                                    cGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcgtc   <  2:729458/139‑1 (MQ=255)

                                                                                                                     gagaTTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcgtcg  <  2:703772/139‑1 (MQ=255)

                                                                                                                      agaTTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCaa                                                                               <  1:741630/61‑1 (MQ=255)

                                                                                                                      agaTTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCaa                                                                               >  2:741630/1‑61 (MQ=255)

                                                                                                                              gtgggtggCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcg     >  1:10512/1‑127 (MQ=255)

                                                                                                                              gtgggtggCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcg     <  2:10512/127‑1 (MQ=255)

GCGCGCCAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGAGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTTCGTCG  >  NC_000913/4054310‑4054565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A