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 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,504,391	T→C	E32G (GAA→GGA)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,504,391	0	T	C	100.0%	192.9 / NA	54	E32G (GAA→GGA)	fryA	putative PTS enzyme: Hpr, enzyme I and IIA components
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/30); total (24/30)

GCCGCGCCTGCTCTTCATCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTTCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGTTAATCAGGA  >  NC_000913/2504257‑2504507

gccgcgccTGCTCTTCATCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCt                                                                                                                  <  1:624790/139‑1 (MQ=255)

     gccTGCTCTTCATCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGcc                                                                                                             <  1:587729/139‑1 (MQ=255)

               cATCGCTGCCGTTAATGTTAAGGCTGCAACTGCCATTAAATAGGGCGCCGGGGCGGACCACGGCCAGGGAAGTTTTCGCATCTGCCTTTGCGTTGTGGCGATGGTTAATAAAAGTGATTCCGCTTCGCCACTGGCTGcc                                                                                                   <  2:209200/139‑2 (MQ=255)

               cATCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAGTAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCg                                                                                                                    <  1:530561/122‑1 (MQ=255)

                aTCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCAc                                                                                                  <  2:4503/139‑1 (MQ=255)

                    cTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGc                                                                                                       >  2:3552/1‑130 (MQ=255)

                    cTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGc                                                                                                       <  1:3552/130‑1 (MQ=255)

                          cTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTaa                                                                                        >  1:159066/1‑139 (MQ=255)

                                       tGCAACTGTCATT‑AATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCGTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGa                                                                          <  1:661232/139‑1 (MQ=255)

                                         cAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGAc                                                                         >  1:876036/1‑139 (MQ=255)

                                         cAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGAc                                                                         >  1:142769/1‑139 (MQ=255)

                                          aaCTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACg                                                                        >  2:802572/1‑139 (MQ=255)

                                          aaCTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACg                                                                        >  1:1078090/1‑139 (MQ=255)

                                          aaCTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACg                                                                        <  2:142769/139‑1 (MQ=255)

                                            cTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAg                                                                      <  2:873548/139‑1 (MQ=255)

                                               tCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCt                                                                                                                  >  1:317042/1‑92 (MQ=255)

                                               tCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCt                                                                                                                  <  2:317042/92‑1 (MQ=255)

                                                  ttAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTa                                                                <  2:1078090/139‑1 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTg                                                                                                     <  2:665254/95‑1 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTg                                                                                                     >  1:665254/1‑95 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCa                                                                                 <  1:999999/115‑1 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCa                                                                                 >  2:999999/1‑115 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGtt                                                         >  2:75239/1‑139 (MQ=255)

                                                         gggTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGtt                                                         >  2:588413/1‑139 (MQ=255)

                                                          ggtgccggtgccAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCa                                                                                                   >  2:626270/1‑96 (MQ=255)

                                                          ggtgccggtgccAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCa                                                                                                   <  1:626270/96‑1 (MQ=255)

                                                                 gtgccAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAg                                                 <  2:178429/139‑1 (MQ=255)

                                                                    ccAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACt                                                                                                          <  1:352750/79‑1 (MQ=255)

                                                                    ccAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACt                                                                                                          >  2:352750/1‑79 (MQ=255)

                                                                            cgcCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCAc                                                                                                  >  1:108023/1‑79 (MQ=255)

                                                                            cgcCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCAc                                                                                                  <  2:108023/79‑1 (MQ=255)

                                                                               cAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGa                                   <  2:876036/139‑1 (MQ=255)

                                                                                         ttCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCa                                                    <  2:701598/112‑1 (MQ=255)

                                                                                         ttCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCa                                                    >  1:701598/1‑112 (MQ=255)

                                                                                            gCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCAc                                                                                                  <  1:591722/63‑1 (MQ=255)

                                                                                            gCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCAc                                                                                                  >  2:591722/1‑63 (MQ=255)

                                                                                               tCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCg                   >  1:161780/1‑139 (MQ=255)

                                                                                                   ccTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTcc               >  2:57134/1‑139 (MQ=255)

                                                                                                   ccTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTcc               <  1:679311/139‑1 (MQ=255)

                                                                                                   ccTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTcc               >  2:679311/1‑139 (MQ=255)

                                                                                                    cTTTGCGGTTTGGCGATTGTTTAAAAAAATTGTTCCGGCTTGGCACTGGCTGCACTGTTCTTTAAGTTCCTACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCg              <  2:157729/139‑1 (MQ=255)

                                                                                                       tGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGt           <  1:984499/139‑1 (MQ=255)

                                                                                                       tGCGTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGt           <  1:75239/139‑1 (MQ=255)

                                                                                                          gTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTa                                                                <  2:295306/83‑1 (MQ=255)

                                                                                                          gTTCTGGCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTa                                                                >  1:295306/1‑83 (MQ=255)

                                                                                                               ggCGATGGTTAATAAAAGTGATTCCGCATTGCCACTGGCAGCATTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAAGTGAATCGTTAACATAACCGCTCCGGGTTAATCAgg   <  2:204012/139‑1 (MQ=255)

                                                                                                                gCGATGGTTAATAAAAGTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGTTAATCAGga  >  2:1023761/1‑139 (MQ=255)

                                                                                                                                gTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGa                                                                          >  1:889714/1‑51 (MQ=255)

                                                                                                                                gTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGa                                                                          <  2:889714/51‑1 (MQ=255)

                                                                                                                                gTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACg                                                                        <  2:617201/53‑1 (MQ=255)

                                                                                                                                gTGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACg                                                                        >  1:617201/1‑53 (MQ=255)

                                                                                                                                 tGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGa                                                                          >  2:807128/1‑50 (MQ=255)

                                                                                                                                 tGATTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGa                                                                          <  1:807128/50‑1 (MQ=255)

                                                                                                                                   aTTCCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGTTa         <  1:718102/113‑1 (MQ=255)

GCCGCGCCTGCTCTTCATCGCTGCCGCTAATGTTCAGGCTGCAACTGTCATTAAATAGGGTGCCGGTGCCAATCAGCGCCAGCGAGCTTTTCGCATCTGCCTTTGCGTTCTGGCGATGGTTAATAAAAGTGATTTCGCTTTGCCACTGGCTGCACTGTTCTTTAAGTTCCCACGCCGGACGAGCATGTAGACCGTTAGGCAAAGGACAGAGAAATTGAATCGTTAACATAACCGCTCCGGGTTAATCAGGA  >  NC_000913/2504257‑2504507

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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