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
A9 F48 I1 R1	82	50.4	1709896	99.0%	1692797	139.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,128,053	C→A	intergenic (‑159/+25)	yiiX ← / ← metJ	putative lipid binding hydrolase/DNA‑binding transcriptional repressor MetJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,128,053	0	C	A	100.0%	138.4 / NA	40	intergenic (‑159/+25)	yiiX/metJ	putative lipid binding hydrolase/DNA‑binding transcriptional repressor MetJ
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (21/19); total (21/19)

GGTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTCCACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGCATCATCCGGC  >  NC_000913/4127920‑4128183

ggTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATTCGGCGTGAACGCCTTATCCTGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTcc                                                                                                                              >  1:204036/1‑140 (MQ=255)

ggTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTcc                                                                                                                              >  1:573289/1‑140 (MQ=255)

 gTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCcg                                                                                                                             >  1:601647/1‑140 (MQ=255)

 gTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCcg                                                                                                                             <  1:368565/140‑1 (MQ=255)

  tGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCATGCGATTACACTCcgc                                                                                                                            >  2:713852/1‑140 (MQ=255)

  tGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACACcgc                                                                                                                            >  1:813876/1‑140 (MQ=255)

         cAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTTTCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGctc                                                                                                                     >  2:529539/1‑140 (MQ=255)

                cGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCttttttt                                                                                                              >  2:127404/1‑139 (MQ=255)

                             tATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTccc                                                                                                 <  2:599941/140‑1 (MQ=255)

                              aTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCa                                                                                                <  1:134510/140‑1 (MQ=255)

                              aTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCa                                                                                                <  1:713852/140‑1 (MQ=255)

                              aTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCa                                                                                                <  2:601647/140‑1 (MQ=255)

                              aTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCa                                                                                                <  1:262188/140‑1 (MQ=255)

                              aTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCa                                                                                                <  1:221399/140‑1 (MQ=255)

                                   ggATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGtct                                                                                           <  1:374510/140‑1 (MQ=255)

                                    gATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGtctc                                                                                          <  1:323018/140‑1 (MQ=255)

                                     aTGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACACCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTcc                                                                                         <  2:813876/140‑1 (MQ=255)

                                              gAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATc                                                                                <  1:745572/140‑1 (MQ=255)

                                                aCGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATccc                                                                              <  2:733302/140‑1 (MQ=255)

                                                aCGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATccc                                                                              <  2:514228/140‑1 (MQ=255)

                                                             ccTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATg                                                                 <  1:437515/140‑1 (MQ=255)

                                                              cTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGa                                                                >  1:652417/1‑140 (MQ=255)

                                                              cTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGa                                                                <  2:52830/140‑1 (MQ=255)

                                                                         tGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGcc                                                     >  1:148690/1‑140 (MQ=255)

                                                                         tGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGcc                                                     >  2:168577/1‑140 (MQ=255)

                                                                         tGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGcc                                                     >  1:295602/1‑140 (MQ=255)

                                                                               ttCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTcc                                               <  2:497688/140‑1 (MQ=255)

                                                                                    tAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGAt                                          >  2:854564/1‑140 (MQ=255)

                                                                                         tGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTtcgt                                     >  2:56789/1‑140 (MQ=255)

                                                                                               atGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTgc                               <  2:148690/140‑1 (MQ=255)

                                                                                               atGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTgc                               <  1:168577/140‑1 (MQ=255)

                                                                                                tGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTgcg                              >  1:163105/1‑140 (MQ=255)

                                                                                                     tAGGCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCtt                         >  2:295523/1‑140 (MQ=255)

                                                                                                        gCCTGATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTAc                      >  1:96321/1‑140 (MQ=255)

                                                                                                            gATAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGTGCTCTTTACGCAg                  >  2:273074/1‑140 (MQ=255)

                                                                                                             aTAAGCGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGa                 >  1:423717/1‑140 (MQ=255)

                                                                                                                  cGTAGCGCATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGc            >  2:637205/1‑140 (MQ=255)

                                                                                                                      gcgcATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGcatca        <  2:359968/140‑1 (MQ=255)

                                                                                                                       cgcATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGcatcat       >  1:801230/1‑140 (MQ=255)

                                                                                                                       cgcATCAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGcatcat       >  1:384609/1‑140 (MQ=255)

                                                                                                                            cAGGCGATTACACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGCATCATCCGGc  >  2:124983/1‑140 (MQ=255)

GGTGGGTCGCAGACAACGTGCTCGTTGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTTCGTGCAAATTCAATAAATTGCAATATGACGTAGGCCTGATAAGCGTAGCGCATCAGGCGATTCCACTCCGCGCCGCTCTTTTTTGCTTTAGTATTCCCACGTCTCCGGGTTAATCCCCATCTCACGCATGATCTCTTTTGCCGCTTCCGGGATTTCGTCGCTGCGCTCTTTACGCAGATCGGCATCATCCGGC  >  NC_000913/4127920‑4128183

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A