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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,078,459	T→C	intergenic (+21/‑838)	yiiD → / → yiiE	GNAT family putative N‑acetyltransferase/CopG family putative transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,078,459	0	T	C	100.0%	104.1 / NA	29	intergenic (+21/‑838)	yiiD/yiiE	GNAT family putative N‑acetyltransferase/CopG family putative transcriptional regulator
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/18); total (11/18)

CGGGTGCAGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCTGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTAAATATTATTTGTAGAACTG  >  NC_000913/4078313‑4078606

cGGGTGCAGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCct                                                                                                                                                 <  1:57233/151‑1 (MQ=255)

 gggTGCAGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCctc                                                                                                                                                >  1:323226/1‑151 (MQ=255)

  ggTGCAGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCctct                                                                                                                                               <  2:131794/151‑1 (MQ=255)

       aGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCa                                                                                                                                           >  1:64625/1‑150 (MQ=255)

                         ttGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTa                                                                                                                         <  2:233245/150‑1 (MQ=255)

                                  agaCGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCt                                                                                                               <  2:222423/151‑1 (MQ=255)

                                           gTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGtt                                                                                                      <  1:392986/151‑1 (MQ=255)

                                             gCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTtat                                                                                                    <  2:136441/151‑1 (MQ=255)

                                               aGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCTGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTatat                                                                                                  >  2:618570/1‑151 (MQ=255)

                                                 tgtTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATAtt                                                                                                 >  1:273865/1‑150 (MQ=255)

                                                             cGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAActct                                                                                    >  2:357110/1‑151 (MQ=255)

                                                             cGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAActct                                                                                    <  1:257829/151‑1 (MQ=255)

                                                                atatCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCtat                                                                                  <  2:73998/150‑1 (MQ=255)

                                                                  atCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATaa                                                                                <  1:68518/150‑1 (MQ=255)

                                                                           cccGCGAAGACATTTGGCCCGTATGAAGAGGGCGGGAAAGAAGAAGAGTAGCTGATGGAGAGGGGCGGGGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAAATTTTAt                                                                        <  2:419272/149‑1 (MQ=255)

                                                                             cgcgAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTAttctt                                                                    <  1:496751/151‑1 (MQ=255)

                                                                              gcgAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTAttcttc                                                                   <  1:470180/151‑1 (MQ=255)

                                                                                  aGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTg                                                               <  1:256558/151‑1 (MQ=255)

                                                                                      aTTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTc                                                           <  2:587552/151‑1 (MQ=255)

                                                                                         tGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCa                                                         <  1:544180/150‑1 (MQ=255)

                                                                                                   gAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTAGATACGTGTc                                                 >  2:533045/1‑148 (MQ=255)

                                                                                                               aaCGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGt                                  >  1:223579/1‑151 (MQ=255)

                                                                                                               aaCGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGt                                  >  1:142939/1‑151 (MQ=255)

                                                                                                                     gaagaGTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGa                            <  2:532285/151‑1 (MQ=255)

                                                                                                                        gagTAGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGc                          >  2:536304/1‑150 (MQ=255)

                                                                                                                            aGCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTa                     <  2:539586/151‑1 (MQ=255)

                                                                                                                             gCTGATGGAGAGGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTa                     >  2:341600/1‑150 (MQ=255)

                                                                                                                                      gagGGGCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTAAATATTAttt           <  2:97815/151‑1 (MQ=255)

                                                                                                                                        ggggCGGTGCCGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTAAATATTATTTGt         >  2:611412/1‑151 (MQ=255)

                                                                                                                                               tgccgcCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTAAATATTATTTGTAGAACTg  >  2:93205/1‑151 (MQ=255)

CGGGTGCAGATGCAGGTCGAAATCTTTGGCGACGAGACGCCGGGTGCAGTGTTTGAAGGCACGTATATCGTTCTGCCCGCGAAGCCATTTGGCCCGTATGAAGAGGGCGGGAACGAAGAAGAGTAGCTGATGGAGAGGGGCGGTGCTGCCTCTCTCATTCAGGTCATTTATATTAGTCCTTGGCTATTTCGGTTATATTAAATAAGAACTCTATAAATTTTTATTCTTCGTTGGCTCCATACGTGTCTTGCTACATCACTGTTCAGGAGCATTTAAATATTATTTGTAGAACTG  >  NC_000913/4078313‑4078606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A