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
A12 F28 I1 R1	121	68.4	2351762	99.3%	2335299	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,417	A→G	intergenic (+40/+22)	rhtC → / ← rhtB	L‑threonine exporter/L‑homoserine/L‑homoserine lactone/L‑threonine exporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,417	0	A	G	100.0%	190.3 / NA	52	intergenic (+40/+22)	rhtC/rhtB	L‑threonine exporter/L‑homoserine/L‑homoserine lactone/L‑threonine exporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (27/25); total (27/25)

GCCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTACGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGT  >  NC_000913/4008286‑4008550

gcCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCAt                                                                                                                               >  1:520794/1‑140 (MQ=255)

 ccGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATc                                                                                                                              >  2:764458/1‑140 (MQ=255)

 ccGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATc                                                                                                                              >  1:73144/1‑140 (MQ=255)

    tGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGa                                                                                                                           >  2:556316/1‑140 (MQ=255)

             aCGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTAtttt                                                                                                                  <  1:924530/140‑1 (MQ=255)

                tCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCa                                                                                                               >  1:842248/1‑140 (MQ=255)

                tCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCa                                                                                                               >  2:614528/1‑140 (MQ=255)

                 cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCa                                                                                                                                <  2:866606/122‑1 (MQ=255)

                 cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCa                                                                                                                                >  1:866606/1‑122 (MQ=255)

                 cTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTACCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCAc                                                                                                              >  2:316481/1‑140 (MQ=255)

                  tGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACg                                                                                                             <  1:556316/140‑1 (MQ=255)

                  tGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACg                                                                                                             <  2:950982/140‑1 (MQ=255)

                    gCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCa                                                                                                           <  1:614528/140‑1 (MQ=255)

                         gTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCt                                                                                                      >  2:945563/1‑140 (MQ=255)

                           ggATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCg                                                                                                    <  2:1123807/140‑1 (MQ=255)

                             aTTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGcc                                                                                                  <  2:851942/140‑1 (MQ=255)

                                  tGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGc                                                                                             >  2:260217/1‑140 (MQ=255)

                                      tttGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAAc                                                                                         >  1:818057/1‑140 (MQ=255)

                                       ttGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACa                                                                                        <  2:830231/140‑1 (MQ=255)

                                            ggggCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCt                                                                                   <  2:54363/140‑1 (MQ=255)

                                                cGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               <  1:688721/140‑1 (MQ=255)

                                                    aTTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAg                                                                           >  2:887055/1‑140 (MQ=255)

                                                       tGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCAt                                                                        >  2:970553/1‑140 (MQ=255)

                                                        gCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATa                                                                       <  1:37149/140‑1 (MQ=255)

                                                             aTTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               >  1:372037/1‑127 (MQ=255)

                                                             aTTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCcca                                                                               <  2:372037/127‑1 (MQ=255)

                                                                   cattcattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGcc                                                            <  2:818057/140‑1 (MQ=255)

                                                                     ttcattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGa                                                          <  1:964462/140‑1 (MQ=255)

                                                                       cattTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGaaa                                                        >  1:941107/1‑140 (MQ=255)

                                                                         tttGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAAt                                                      >  1:41164/1‑140 (MQ=255)

                                                                                  ttCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAg                                             >  2:1110665/1‑140 (MQ=255)

                                                                                      cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         >  2:571879/1‑140 (MQ=255)

                                                                                      cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         <  1:970553/140‑1 (MQ=255)

                                                                                      cgGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGcc                                         >  1:861389/1‑140 (MQ=255)

                                                                                       ggTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCt                                        >  2:520753/1‑140 (MQ=255)

                                                                                       ggTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCt                                        >  2:117053/1‑140 (MQ=255)

                                                                                           aTGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCAt                                    >  1:46782/1‑140 (MQ=255)

                                                                                                    gcgTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  2:491308/140‑1 (MQ=255)

                                                                                                    gcgTCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  1:571879/140‑1 (MQ=255)

                                                                                                       tCTTCAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTcc                        >  1:730896/1‑140 (MQ=255)

                                                                                                           cAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTa                    <  2:73144/140‑1 (MQ=255)

                                                                                                           cAGAGTAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAACAGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTa                    <  1:632325/140‑1 (MQ=255)

                                                                                                                tAAGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCa               <  1:117053/140‑1 (MQ=255)

                                                                                                                  aGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATa             >  2:242419/1‑140 (MQ=255)

                                                                                                                  aGTCGGATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATa             >  1:1124737/1‑140 (MQ=255)

                                                                                                                    tCGGGTAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           >  2:523260/1‑124 (MQ=255)

                                                                                                                    tCGGGTAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTgg                           <  1:523260/124‑1 (MQ=255)

                                                                                                                       gATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCa        <  1:242419/140‑1 (MQ=255)

                                                                                                                       gATAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCa        <  1:945563/140‑1 (MQ=255)

                                                                                                                         tAAGGCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCCCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAAt      <  1:113100/140‑1 (MQ=255)

                                                                                                                            ggCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCg   <  2:520794/140‑1 (MQ=255)

                                                                                                                             gCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGt  <  1:260217/140‑1 (MQ=255)

                                                                                                                             gCGTTTGCGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGt  >  2:226709/1‑140 (MQ=255)

GCCGTGGTTATCAACGTCTGGCGAAGTGGATTGATGGTTTTGCCGGGGCGTTATTTGCCGGATTTGGCATTCATTTGATTATTTCGCGGTGATGCCAGACGCGTCTTCAGAGTAAGTCGGATAAGGCGTTTACGCCGCATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCCTTTAATCCATAGAGCAATCCGT  >  NC_000913/4008286‑4008550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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