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
A20 F60 I1 R1	17	55.4	1884452	98.9%	1863723	138.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,562,053	C→A	intergenic (+60/‑58)	yffN → / → yffO	CPZ‑55 prophage; uncharacterized protein YffN/CPZ‑55 prophage; uncharacterized protein YffO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,562,053	0	C	A	100.0%	150.2 / NA	43	intergenic (+60/‑58)	yffN/yffO	CPZ‑55 prophage; uncharacterized protein YffN/CPZ‑55 prophage; uncharacterized protein YffO
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (25/18); total (25/18)

TGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTCAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGCCA  >  NC_000913/2561920‑2562188

tGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCt                                                                                                                                   >  1:845903/1‑140 (MQ=255)

      tGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGaa                                                                                                                             >  1:493996/1‑140 (MQ=255)

        gTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGaaaa                                                                                                                           >  1:244360/1‑140 (MQ=255)

        gTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGaaaa                                                                                                                           >  2:238060/1‑140 (MQ=255)

        gTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGaaaa                                                                                                                           <  2:149899/140‑1 (MQ=255)

             cGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGCTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGc                                                                                                                      >  1:606440/1‑140 (MQ=255)

                aaTCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCaaa                                                                                                                   <  2:377486/140‑1 (MQ=255)

                  tCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCaaaaa                                                                                                                 >  2:534365/1‑140 (MQ=255)

                        gAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACgg                                                                                                           >  1:267439/1‑140 (MQ=255)

                          aTTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTa                                                                                                         >  1:496154/1‑140 (MQ=255)

                          aTTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTa                                                                                                         >  1:513485/1‑140 (MQ=255)

                              cTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTAtttt                                                                                                     >  1:95069/1‑140 (MQ=255)

                                agagATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTtc                                                                                                   <  1:337170/140‑1 (MQ=255)

                                agagATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTtc                                                                                                   <  2:493996/140‑1 (MQ=255)

                                agagATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTtc                                                                                                   >  2:337170/1‑140 (MQ=255)

                                  agaTTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTtcat                                                                                                 <  1:238060/140‑1 (MQ=255)

                                            gcgcCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTgg                                                                                       <  2:939397/140‑1 (MQ=255)

                                              gcCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAA‑TAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTgg                                                                                       <  1:932755/137‑1 (MQ=255)

                                              gcCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAA‑TAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTgg                                                                                       >  2:932755/1‑137 (MQ=255)

                                                       cGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATgg                                                                            <  2:496154/140‑1 (MQ=255)

                                                         cTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGaa                                                                          <  2:95069/140‑1 (MQ=255)

                                                           ccGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAgg                                                                        <  2:606440/140‑1 (MQ=255)

                                                                aGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAAc                                                                   <  2:244360/140‑1 (MQ=255)

                                                                         aCGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGaaa                                                          >  2:581250/1‑140 (MQ=255)

                                                                                     gcgcTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAg                                              >  1:884607/1‑140 (MQ=255)

                                                                                        cTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACa                                           <  1:534365/140‑1 (MQ=255)

                                                                                                   ggTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAg                                              <  2:37489/126‑1 (MQ=255)

                                                                                                   ggTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAg                                              >  1:37489/1‑126 (MQ=255)

                                                                                                   ggTAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACAcc                                >  1:936811/1‑140 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAg                                              <  1:685773/124‑1 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAg                                              >  2:685773/1‑124 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAg                              >  2:283057/1‑140 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAg                              >  2:779257/1‑140 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAg                              >  2:61373/1‑140 (MQ=255)

                                                                                                     tAATTATTGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGGTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAg                              >  2:820772/1‑140 (MQ=255)

                                                                                                       attattGCGGTTTTTGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCg                            >  2:459050/1‑140 (MQ=255)

                                                                                                                   tttGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGaaaa                >  1:39553/1‑140 (MQ=255)

                                                                                                                     tGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAaca                       >  2:186526/1‑131 (MQ=255)

                                                                                                                     tGTCAATTTTCAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAaca                       <  1:186526/131‑1 (MQ=255)

                                                                                                                               cAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGc    <  1:61373/140‑1 (MQ=255)

                                                                                                                               cAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGc    <  2:513485/140‑1 (MQ=255)

                                                                                                                               cAACCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGc    <  1:779257/140‑1 (MQ=255)

                                                                                                                                 aCCTAAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGCCa  >  1:356651/1‑140 (MQ=255)

TGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAATTATTGCGGTTTTTGTCAATTTTCAACCTCAATTCTTGCGAAAAATGGCAAAAATAACGGTATTTTTCATCATTTATTGGGGGTTTTATGGAAGGCGAACTGATAGAAAACAATGGGTTAGACATTTATGACACCAGCGAAACACCGAAAAAGCGCGGTCGGCCA  >  NC_000913/2561920‑2562188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A