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
A10 F1 I1 R1	77	35.1	1569012	96.6%	1515665	112.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,346,060	A→G	E448E (GAA→GAG)	rpoN →	RNA polymerase, sigma 54 (sigma N) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,346,060	0	A	G	100.0%	131.5 / NA	36	E448E (GAA→GAG)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/19); total (17/19)

TTTCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAACAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATG  >  NC_000913/3345924‑3346175

tttCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCa                                                                                                                   >  2:615106/1‑139 (MQ=255)

tttCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCa                                                                                                                   <  2:351534/139‑1 (MQ=255)

      gTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTAt                                                                                                             >  1:426552/1‑139 (MQ=255)

                tACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCa                                                                                                   >  1:144833/1‑139 (MQ=255)

                tACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCa                                                                                                   <  2:677138/139‑1 (MQ=255)

                     aGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCAcgccg                                                                                              >  1:36122/1‑139 (MQ=255)

                       ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            >  2:703627/1‑139 (MQ=255)

                       ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            <  2:651993/139‑1 (MQ=255)

                       ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            <  1:703627/139‑1 (MQ=255)

                       ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            >  1:488356/1‑139 (MQ=255)

                        gcggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           <  2:653268/139‑1 (MQ=255)

                         cggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACt                                                                                          >  2:468587/1‑139 (MQ=255)

                          ggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTg                                                                                         <  1:468587/139‑1 (MQ=255)

                               cgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    <  1:615106/139‑1 (MQ=255)

                                gatgCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTACCCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGa                                                                                   <  2:268222/136‑1 (MQ=255)

                                  aGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAg                                                                                 <  2:426552/139‑1 (MQ=255)

                                         tccACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          <  2:144833/139‑1 (MQ=255)

                                                         cgcTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTct                                                          <  2:488356/139‑2 (MQ=255)

                                                                   gaaATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAAc                                                >  1:106331/1‑139 (MQ=255)

                                                                   gaaATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAAc                                                >  2:641167/1‑139 (MQ=255)

                                                                        tAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCaaa                                                 <  2:232357/133‑1 (MQ=255)

                                                                        tAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCaaa                                                 >  1:232357/1‑133 (MQ=255)

                                                                          aTCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTa                                         <  2:249514/139‑1 (MQ=255)

                                                                                    aaaaCCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    <  2:577449/86‑1 (MQ=255)

                                                                                    aaaaCCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    >  1:577449/1‑86 (MQ=255)

                                                                                           aGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGAccc                        >  1:743583/1‑139 (MQ=255)

                                                                                                          cGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          <  2:23698/74‑1 (MQ=255)

                                                                                                          cGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          >  1:23698/1‑74 (MQ=255)

                                                                                                            aCAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGaca       >  2:426655/1‑139 (MQ=255)

                                                                                                                cAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGt                                                                                >  1:206423/1‑62 (MQ=255)

                                                                                                                cAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGt                                                                                <  2:206423/62‑1 (MQ=255)

                                                                                                                 aaGTTAACCTCTTTGCTGTCGGAGAAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATg  <  2:587867/139‑1 (MQ=255)

                                                                                                                   gTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           <  1:576386/48‑1 (MQ=255)

                                                                                                                   gTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           >  2:576386/1‑48 (MQ=255)

                                                                                                                    ttAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCg                   >  1:338224/1‑119 (MQ=255)

                                                                                                                    ttAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCg                   <  2:338224/119‑1 (MQ=255)

TTTCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAACAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATG  >  NC_000913/3345924‑3346175

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A