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
A28 F1 I1 R1	15	45.6	2893554	96.7%	2798066	76.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	4,108,507	T→G	intergenic (‑5/‑272)	metJ ← / → metB	transcriptional repressor protein MetJ/cystathionine gamma‑synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	4,108,507	0	T	G	100.0%	115.7 / NA	29	intergenic (‑5/‑272)	metJ/metB	transcriptional repressor protein MetJ/cystathionine gamma‑synthase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (14/15); total (14/15)

ACTTGTTCACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGATACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCGCAT  >  REL606/4108438‑4108579

aCTTGTTCTCTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGCGAGACTTaa                                                                    >  1:43043/1‑76 (MQ=255)

aCTTGTTCACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTaa                                                                    <  1:590809/76‑1 (MQ=255)

  ttGTTCACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATc                                                                  >  2:122065/1‑76 (MQ=255)

      tCACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCctct                                                              <  1:768457/76‑1 (MQ=255)

       cACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCtt                                                             <  1:909383/76‑1 (MQ=255)

         ctctTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCg                                                           >  1:760187/1‑76 (MQ=255)

         ctctTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCg                                                           >  1:760163/1‑76 (MQ=255)

           cttcttGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTc                                                         <  2:936180/76‑1 (MQ=255)

           cttcttGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTc                                                         >  2:239809/1‑76 (MQ=255)

             tcttGCCGAGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCaa                                                       >  1:53307/1‑76 (MQ=255)

              cttGNCGTGCTCAGCGTATGGGCGGATATATACGCCGCTNCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAAt                                                      <  1:177853/76‑1 (MQ=255)

              cttGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAAt                                                      <  1:391313/76‑1 (MQ=255)

               ttGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATa                                                     <  1:986576/76‑1 (MQ=255)

                 gCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATaaa                                                   >  2:562815/1‑76 (MQ=255)

                         cAGCTTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGagacc                                           >  2:1424957/1‑76 (MQ=255)

                             gTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGagaccagac                                       >  2:492649/1‑76 (MQ=255)

                              tATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGagaccagacc                                      <  1:946962/76‑1 (MQ=255)

                               aTGGGCTGATATAATCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAgaccagacca                                     <  1:426157/76‑1 (MQ=255)

                                      gATATATTCGCCGCTCCATTCAGCCATGAGAGACTTNATCCTCTTCGACAATCAATTGAGACCAGACCACANAGtt                              >  1:181920/1‑76 (MQ=255)

                                         atatTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGAt                           >  1:234100/1‑76 (MQ=255)

                                          tatTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGAtg                          <  2:1122247/76‑1 (MQ=255)

                                           atTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACTAGACNACACAGTTGAtgt                         >  2:1323197/1‑76 (MQ=255)

                                           atTCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGAtgt                         <  1:394994/76‑1 (MQ=255)

                                             tCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTgg                       <  1:902749/76‑1 (MQ=255)

                                             tCGCCGCTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTgg                       <  1:384160/76‑1 (MQ=255)

                                                ccgcTCCATTCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTa                    >  1:917094/1‑76 (MQ=255)

                                                         tCAGCCATGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTa           <  1:637044/76‑1 (MQ=255)

                                                               aTGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCg     <  1:835400/76‑1 (MQ=255)

                                                               aTGAGAGACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCg     >  2:704795/1‑76 (MQ=255)

                                                                 gagagaCTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCGCa   <  1:122065/76‑1 (MQ=255)

                                                                  agagACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCGCAt  <  1:238571/76‑1 (MQ=255)

ACTTGTTCACTCTTCTTGCCGTGCTCAGCGTATGGGCTGATATATTCGCCGCTCCATTCAGCCATGAGATACTTAATCCTCTTCGTCAATAAATTGAGACCAGACCACACAGTTGATGTGGGTACTGACCGTAAACCCGCAT  >  REL606/4108438‑4108579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A