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	2,522,472	T→C	E2E (GAA→GAG)	xapR ←	transcriptional activator of xapAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,522,472	0	T	C	100.0%	186.3 / NA	50	E2E (GAA→GAG)	xapR	transcriptional activator of xapAB
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/32); total (18/32)

CGTGCCGAGTTGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGTTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCAAGCGCACGA  >  NC_000913/2522325‑2522618

cGTGCCGAGTTGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTcc                                                                                                                                                 <  2:618039/151‑1 (MQ=255)

    ccGAGTTGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATa                                                                                                                                              >  1:540177/1‑150 (MQ=255)

        gTTGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTaa                                                                                                                                         <  2:540182/151‑1 (MQ=255)

          tGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAg                                                                                                                                        <  2:86735/150‑1 (MQ=255)

          tGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAg                                                                                                                                        <  2:430759/150‑1 (MQ=255)

            aTTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGc                                                                                                                                     <  1:121467/151‑1 (MQ=255)

               ttCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTcc                                                                                                                                  >  2:481097/1‑151 (MQ=255)

                 ccAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGATATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCa                                                                                                                                 <  2:550297/150‑1 (MQ=255)

                 ccAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCat                                                                                                                                <  1:254593/151‑1 (MQ=255)

                 ccAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCat                                                                                                                                <  2:404256/151‑1 (MQ=255)

                  cAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCata                                                                                                                               <  2:81591/151‑1 (MQ=255)

                  cAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCat                                                                                                                                >  1:71359/1‑150 (MQ=255)

                   aGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCatat                                                                                                                              >  2:642010/1‑151 (MQ=255)

                   aGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCatat                                                                                                                              >  2:3589/1‑151 (MQ=255)

                         ttAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATAtaataa                                                                                                                         <  2:16796/150‑1 (MQ=255)

                              atGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACAt                                                                                                                   >  2:249114/1‑151 (MQ=255)

                              atGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACAt                                                                                                                   <  2:211304/151‑1 (MQ=255)

                                    gCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTAtt                                                                                                             >  2:579706/1‑151 (MQ=255)

                                       gAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTa                                                                                                            <  1:15681/149‑1 (MQ=255)

                                        aGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTaa                                                                                                           <  1:410057/149‑1 (MQ=255)

                                          cGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTa                                                                                                       <  1:243209/151‑1 (MQ=255)

                                                  gagaCATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCCTCCGCTACGGCAAGAAAATAACGGAGCAAATTAAGATCTGTTCTGTATACTCGCTCCATAATTAAGTGCGCCATATAATAAATACATCTTATTAAATTATCATgg                                                                                                 <  1:386635/149‑1 (MQ=255)

                                                         atTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGt                                                                                         >  1:645474/1‑150 (MQ=255)

                                                                         gcgcGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGatat                                                                        >  1:516930/1‑151 (MQ=255)

                                                                         gcgcGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGata                                                                         <  1:290599/150‑1 (MQ=255)

                                                                         gcgcGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGat                                                                          <  2:583642/149‑1 (MQ=255)

                                                                           gcgGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATcc                                                                      >  2:122932/1‑151 (MQ=255)

                                                                                cAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGacat                                                                 >  2:52154/1‑151 (MQ=255)

                                                                                  aaaTGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGacatac                                                               >  2:514988/1‑151 (MQ=255)

                                                                                   aaTGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGacataca                                                              <  2:434807/151‑1 (MQ=255)

                                                                                      gCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGAcatacata                                                            <  1:516943/150‑1 (MQ=255)

                                                                                      gCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATaa                                                           <  1:403691/151‑1 (MQ=255)

                                                                                            ctTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAAcaca                                                      >  1:587263/1‑150 (MQ=255)

                                                                                              tCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAAcaca                                                      <  1:453792/148‑1 (MQ=255)

                                                                                              tCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACaa                                                     <  1:209292/149‑1 (MQ=255)

                                                                                                  cTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGat                                                >  2:489569/1‑150 (MQ=255)

                                                                                                    aCGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGata                                               <  1:279927/149‑1 (MQ=255)

                                                                                                    aCGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGata                                               <  2:567477/149‑1 (MQ=255)

                                                                                                    aCGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGata                                               <  1:332414/149‑1 (MQ=255)

                                                                                                      ggCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAatat                                           <  1:249113/151‑1 (MQ=255)

                                                                                                           gAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCATATATCCGACATACATAAACACAATGGATAATATACCCg                                      <  1:652595/151‑1 (MQ=255)

                                                                                                                 aaCGGAGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAAt                                 <  1:43947/150‑1 (MQ=255)

                                                                                                                      aGCAACTTAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACAttt                           <  2:326069/151‑1 (MQ=255)

                                                                                                                            ttAAGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTAc                      >  1:364944/1‑150 (MQ=255)

                                                                                                                              aaGATCTGTTCTGTATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAgg                   <  2:74652/151‑1 (MQ=255)

                                                                                                                                    tgttctgtATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAg              >  1:350711/1‑150 (MQ=255)

                                                                                                                                       tctgtATACGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCa           >  2:30698/1‑150 (MQ=255)

                                                                                                                                           tataCGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCAAgc        <  1:522919/149‑1 (MQ=255)

                                                                                                                                              aCGCGCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCAAGCGCACg   >  1:27792/1‑151 (MQ=255)

                                                                                                                                               cgcgCTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCAAGCGCACGa  <  1:202470/151‑1 (MQ=255)

CGTGCCGAGTTGATTTTCCAGCTCTTTAATATGAATGCTGAGCGGAGGCTGAGACATATTTAAACGCGCTGCTGCGCGGCCAAAATGCAACTCTTCCGCTACGGCAAGAAAATAACGGAGCAACTTAAGATCTGTTCTGTATACGCGTTCCATAATTAAGTGCTCCATATAATAAATACATCGTATTAAATTATCATGGCATAAAGTATTTCACCACCAGATATCCGACATACATAAACACAATGGATAATATACCCGGTAATACATTTGGTACAGGAATAGGCAAGCGCACGA  >  NC_000913/2522325‑2522618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A