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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	629,681	C→A	100%	L84I (CTA→ATA)	hxlA →	possible 3‑hexulose‑6‑phosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	629,681	0	C	A	100.0%	129.7 / NA	43	L84I (CTA→ATA)	hxlA	possible 3‑hexulose‑6‑phosphate synthase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (29/14); total (29/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTG  >  CP000730/629548‑629816

atgtacaacagcagTAAAACACATGAGATACAATATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGgtgt                                                                                                                                  <  2:370097/133‑1 (MQ=255)

 gggtgaCCAGCAGGTAAACATATGGCAGACAACATTCAGAATGTAAAATTATGGGCAGGCATGAAAATTATAGATGCAGCTGATCATGAAGTTAGCCAAGCAAGTAAATTTGGCGCGGATGTAATTACAATGATAGGTGtt                                                                                                                                 >  2:285613/6‑141 (MQ=255)

            aggtAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGAAGAAGATGc                                                                                                                      >  2:447376/4‑141 (MQ=255)

            agTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGc                                                                                                                      >  1:35726/1‑141 (MQ=255)

                         gCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGTAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAagca                                                                                                         <  2:197844/141‑1 (MQ=255)

                           aGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAagcagc                                                                                                       >  1:494887/1‑141 (MQ=255)

                            gACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCt                                                                                                      <  2:210345/141‑1 (MQ=255)

                                             acaaGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGAGTTCCAGAAGATGCATCAATTAAAACAGCTATAGAAGAAGCCCATaa                                                                                     >  2:130558/3‑141 (MQ=255)

                                                    ttAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCACTTAAAGCAGCTATTGAAGAAGCTCATAAAaataat                                                                              >  1:147111/1‑141 (MQ=255)

                                                     tAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAataata                                                                             >  1:527777/1‑141 (MQ=255)

                                                     tAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAataata                                                                             >  2:134451/1‑141 (MQ=255)

                                                       gCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCAGAAAAATAATaaa                                                                           >  2:290715/1‑141 (MQ=255)

                                                        cAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCCCATAAAAATAATAAAc                                                                          >  2:338503/1‑141 (MQ=255)

                                                           ccATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACCATAATAGGTGTTGCAGAAGATGCGTCAATTAAAGCAGCTATTGAAGAAGCTCATAAACATAATAACCAAt                                                                       >  2:368555/2‑141 (MQ=255)

                                                           aCATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCGGTTATTGAAGAAGCTCTTAAAAATAATAAACAAt                                                                       >  1:22096/1‑141 (MQ=255)

                                                                 aaaTTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAg                                                                 >  1:120018/1‑141 (MQ=255)

                                                                 aaaTGATGGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAg                                                                 <  2:85967/141‑1 (MQ=255)

                                                                         gATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATg                                                         >  1:158690/1‑141 (MQ=255)

                                                                           tGCAGCTGATTATGTAGGTAGCCAAGCAATTAAATTTGGCGCGGACGTAATTACAATAATAGGTGTAGCAGACGATGCATCAATTGAAGGAGCTATTGAAGAAGCTCATAAAAATAATAAACAAGTACTAGTTGATATGAt                                                       <  2:261700/141‑1 (MQ=255)

                                                                           tGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGAAGAAGATGCATCAATTAAAGCAGTTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGAt                                                       <  2:261703/141‑1 (MQ=255)

                                                                            gCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGAtt                                                      <  2:259513/141‑1 (MQ=255)

                                                                               gCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAACTAATAAACAATTACTAGATGATATGATTGCt                                                   >  2:300565/1‑141 (MQ=255)

                                                                               gCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCt                                                   >  1:39325/1‑141 (MQ=255)

                                                                                  gATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGtt                                                >  1:508537/1‑141 (MQ=255)

                                                                                  gATTATGAAGTTAGCCAAGCAATTAAATTTGAAGCGGATGTAATTACAATAATAGGTGTTGAAGAAGATGAATCAATTAAAGCAGCTATTGAAAAAGCTCATAAAAATAATAACAAATTACTAGTTAATATGATTACTGtt                                                >  2:533843/1‑141 (MQ=255)

                                                                                   aTTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTc                                               >  2:73512/1‑141 (MQ=255)

                                                                                         aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGAtt                                         >  1:254481/1‑141 (MQ=255)

                                                                                         aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGAtt                                         <  2:494887/141‑1 (MQ=255)

                                                                                         aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGAtt                                         <  2:524735/141‑1 (MQ=255)

                                                                                         aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTAAAGaat                                         >  2:535902/1‑139 (MQ=255)

                                                                                             tAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATATAGa                                     >  2:560575/1‑141 (MQ=255)

                                                                                               gCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGaaa                                   <  1:77344/141‑1 (MQ=255)

                                                                                                ccAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGaaaa                                  >  2:326786/1‑141 (MQ=255)

                                                                                                    gCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATGGCTGTTCAAGATTTAGAAAAACGt                              >  2:102659/1‑141 (MQ=255)

                                                                                                       aTTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTAAAGATTTAGAAAAACGTGCa                           >  2:256218/1‑141 (MQ=255)

                                                                                                        ttAAATTTGGCGCGGATGTAAAAACAAAAAAAGGTGTTGCAGAAGATGCAGAAATTAAAGCAGCTATTGAAGAAGCTCATAAAAACAATAAACAATTACTAGTTGATATGATTGCTGTAAAAAAAAAAAAAAAACGTGCaa                          <  2:416836/141‑1 (MQ=255)

                                                                                                           aaTTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAg                       >  1:63591/1‑141 (MQ=255)

                                                                                                            aTTTGGCGCGGATGTAATTAGAATAATAGGTGTTGCAGAAGATGCATCAATTAACGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGa                      >  1:369847/1‑141 (MQ=255)

                                                                                                             tttggcatgtgtGTAATTACGATAATAGGTGTTGTATAAGATGCATCAATTAAAGCAGCCATTGAAGATGCTCATAAAAATAAGAAACGATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGaa                     <  2:30156/130‑1 (MQ=255)

                                                                                                                ggCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGCACTa                  >  2:82105/1‑141 (MQ=255)

                                                                                                                ggCGCGGATCTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATGAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTa                  >  2:366656/1‑141 (MQ=255)

                                                                                                                     ggATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGa             <  1:311632/141‑1 (MQ=255)

                                                                                                                      gATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAAATACTAGTTGATATGATTGCTGTTCAAGATTTAGAACAACGTGCAAAAGAACTAGATGaa            <  2:553348/141‑1 (MQ=255)

                                                                                                                                aaataatAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTg  <  1:305018/140‑1 (MQ=255)

AGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTG  >  CP000730/629548‑629816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A