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
A1 F21 I1 R6	776	393.9	12922803	98.2%	12690192	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	3,269,697	G→A	G200S (GGT→AGT)	yhaC →	YhaC family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	3,269,697	0	G	A	100.0%	86.9 / NA	24	G200S (GGT→AGT)	yhaC	YhaC family protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (12/12); total (12/12)

TCTGGACTTACGTAATGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTGGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACAT  >  NZ_CP025268/3269564‑3269830

tctGGACTTACGTAATGTCGATTTAGATTATTATGATTTCACATATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTcta                                                                                                                                 >  2:936046/1‑138 (MQ=255)

              aTGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCcaca                                                                                                                   <  2:5071178/140‑1 (MQ=255)

               tGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACaa                                                                                                                  >  1:4205633/1‑140 (MQ=255)

                    aTTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTcc                                                                                                             >  2:950735/1‑140 (MQ=255)

                                   aTTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTa                                                                                              <  2:4164759/140‑1 (MQ=255)

                                   aTTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTACAGGTTAATTTTGTTAGTACAACACAAAACGCCACAATCTCCTGGGATTATTTACTa                                                                                              <  1:2390248/140‑1 (MQ=255)

                                                      ggCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTtaa                                                                           >  1:6281549/1‑140 (MQ=255)

                                                        cTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTtaata                                                                         <  1:5398645/140‑1 (MQ=255)

                                                          aaTACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAg                                                                       >  1:1747593/1‑140 (MQ=255)

                                                                 ttttAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGc                                                                >  1:384081/1‑140 (MQ=255)

                                                                                     aaTTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCAt                                                                    >  1:4057867/1‑116 (MQ=255)

                                                                                     aaTTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCAt                                                                    <  2:4057867/116‑1 (MQ=255)

                                                                                     aaTTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGa                                                              <  1:6091578/122‑1 (MQ=255)

                                                                                     aaTTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGa                                                              >  2:6091577/1‑122 (MQ=255)

                                                                                     aaTTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGaaaa                                            >  2:184949/1‑140 (MQ=255)

                                                                                             aaaTTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTAATAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGt                                    <  1:3434113/140‑1 (MQ=255)

                                                                                                               cATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAg                          >  1:4481549/1‑132 (MQ=255)

                                                                                                               cATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAg                          <  2:4481549/132‑1 (MQ=255)

                                                                                                                  gTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATg               <  1:2225260/140‑1 (MQ=255)

                                                                                                                   tttCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGa              >  1:4846183/1‑140 (MQ=255)

                                                                                                                          ttAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGga       <  2:4205633/140‑1 (MQ=255)

                                                                                                                            aaTTTTGTTATTTAAACAAAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAAAGCCTGTTTTAATAAGCAGTAGCGATTTGTATTATGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGATCATGgaga     >  2:3536617/1‑140 (MQ=255)

                                                                                                                             aTTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGAc    <  1:3293146/140‑1 (MQ=255)

                                                                                                                               tttGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACAt  <  1:950735/140‑1 (MQ=255)

TCTGGACTTACGTAATGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTGGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACAT  >  NZ_CP025268/3269564‑3269830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 11 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GACTTACGTAATGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTGGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGAAGAAC  >  NZ_CP025268/3269568‑3269841

GACTTACGTAATGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAA                                                                                                                             >  SRR14920171.4224866/1‑151 (MQ=60)

                               ATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTACAGGTTAATTTTGTTAGTACAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCC                                                                                              <  SRR14920171.2401103/151‑1 (MQ=60)

                                       GATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAA                                                                                      >  SRR14920171.6312623/1‑151 (MQ=60)

                                           AACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAG                                                                                  >  SRR14920171.1755427/1‑151 (MQ=60)

                                                  GGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGC                                                                           >  SRR14920171.385830/1‑151 (MQ=60)

                                                    CTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGA                                                                         <  SRR14920171.5423467/151‑1 (MQ=60)

                                                               gagacagCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTG                                                              <  SRR14920171.6121369/144‑1 (MQ=60)

                                                                      CTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTctgtctcttatac                                                       >  SRR14920171.4076453/1‑138 (MQ=60)

                                                                               tcaataaAACAATTTTTAATAATGCCAACATGTTGCTGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTT                                              <  SRR14920171.1924164/144‑1 (MQ=60)

                                                                                         AAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTAATAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGT                                    <  SRR14920171.3449804/151‑1 (MQ=60)

                                                                                                ACTAATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAA                             >  SRR14920171.4501993/1‑151 (MQ=60)

                                                                                                    ATGCCAACATGTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGA                         >  SRR14920171.4868420/1‑151 (MQ=60)

                                                                                                              GTTTCAGGTTAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGAC               <  SRR14920171.2235429/151‑1 (MQ=60)

                                                                                                                      agAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGA       <  SRR14920171.3654539/149‑1 (MQ=60)

                                                                                                                      agAATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGA       <  SRR14920171.2815539/149‑1 (MQ=60)

                                                                                                                         ATTTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGAAGA    <  SRR14920171.3308146/151‑1 (MQ=60)

                                                                                                                           TTTGTTAGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGAAGAAC  <  SRR14920171.955027/151‑1 (MQ=60)

GACTTACGTAATGTCGATTTAGATTATTATGATTTCACAGATAAACATATGGCTAATACTATTTTAAATCCTTTTAAATTGAATTCAACAAATTTTACTAATGCCAACATGTTTCAGGTTAATTTTGTTGGTTCAACACAAAACGCCACAATCTCCTGGGATTATTTACTAAAAATAACGCCTGTTTTAATAAGCATTAGCGATATGTATTCTGAAGAAAAAATCAAGTTTGTCGAAAGTTGTTTAAATGAGCCTGGAGACATTACCGAAGAAC  >  NZ_CP025268/3269568‑3269841

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 11 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`