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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,360,769	G→A	intergenic (+153/‑407)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,360,769	0	G	A	100.0%	169.5 / NA	52	intergenic (+153/‑407)	gltD/gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/29); total (23/29)

GCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATA  >  NC_000913/3360651‑3360894

gCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           >  2:979607/1‑139 (MQ=255)

gCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           <  1:229157/139‑1 (MQ=255)

    aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           <  2:893346/135‑1 (MQ=255)

    aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           >  1:893346/1‑135 (MQ=255)

    aTCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                       <  2:960968/139‑1 (MQ=255)

                        cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACa                                                                                               >  2:876509/1‑127 (MQ=255)

                        cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACa                                                                                               <  1:876509/127‑1 (MQ=255)

                        cgcgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                   <  1:979607/139‑1 (MQ=255)

                          cgTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTa                                                                                 >  1:1103149/1‑139 (MQ=255)

                                  tCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                           >  2:961332/1‑121 (MQ=255)

                                  tCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATcc                                                                                           <  1:961332/121‑1 (MQ=255)

                                  tCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                         <  1:263378/139‑1 (MQ=255)

                                      gCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                     <  1:953003/139‑1 (MQ=255)

                                         aaTGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACctct                                                                  >  2:319568/1‑139 (MQ=255)

                                                cATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                     >  2:149735/1‑129 (MQ=255)

                                                cATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACAcc                                                                     <  1:149735/129‑1 (MQ=255)

                                                          tGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                    >  1:38301/1‑120 (MQ=255)

                                                          tGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACct                                                                    <  2:38301/120‑1 (MQ=255)

                                                           gACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCa                                                <  1:1061025/139‑1 (MQ=255)

                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGc                                                 >  2:1022745/1‑132 (MQ=255)

                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGc                                                 <  1:1022745/132‑1 (MQ=255)

                                                                 tCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTAt                                          >  2:417594/1‑139 (MQ=255)

                                                                     ataataGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAg                                      <  1:319568/139‑1 (MQ=255)

                                                                           gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                       >  1:178898/1‑68 (MQ=255)

                                                                           gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTtct                                                                                                       <  2:178898/68‑1 (MQ=255)

                                                                           gggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCtttt                                >  2:493705/1‑139 (MQ=255)

                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           <  1:43024/63‑1 (MQ=255)

                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAt                                                                                                           >  2:43024/1‑63 (MQ=255)

                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                               >  1:959304/1‑139 (MQ=255)

                                                                            ggATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTc                               >  2:116865/1‑139 (MQ=255)

                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                         <  2:550198/96‑1 (MQ=255)

                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTaa                                                                         >  1:550198/1‑96 (MQ=255)

                                                                             gATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCa                              <  1:417594/139‑1 (MQ=255)

                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                        <  1:493551/128‑1 (MQ=255)

                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTc                                        >  2:493551/1‑128 (MQ=255)

                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAt                             <  1:430851/139‑1 (MQ=255)

                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAt                             >  2:430851/1‑139 (MQ=255)

                                                                              aTAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCATCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCAt                             >  2:704286/1‑139 (MQ=255)

                                                                                aaTTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                           <  2:959304/139‑1 (MQ=255)

                                                                                        aTAAATTGTGCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAAGTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTaaa                   <  1:704286/139‑1 (MQ=255)

                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTCCAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct             <  1:493705/139‑1 (MQ=255)

                                                                                              tgtgCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGtct             <  1:116865/139‑1 (MQ=255)

                                                                                                 gCTTTGTTCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGa          <  2:1103149/139‑1 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                   >  2:873912/1‑60 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAAt                                                                                   <  1:873912/60‑1 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGc                                                 <  1:146323/94‑1 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGc                                                 >  2:146323/1‑94 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTaaa                   <  2:973691/124‑1 (MQ=255)

                                                                                                       ttCACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTaaa                   >  1:973691/1‑124 (MQ=255)

                                                                                                         cACCAAGTCTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAata  <  2:580685/139‑1 (MQ=255)

                                                                                                                 cTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                           <  1:819094/106‑1 (MQ=255)

                                                                                                                 cTGATAAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTc                           >  2:819094/1‑106 (MQ=255)

GCGAATCAAATTACTGACGAAGTGCGCGTTGTTTTCTGGCAAATGCGGCATGAGCGTTTGACCTTTCCTATAATAGGGATAATTTTCAATAAATTGTGCTTTGTTCACCAAGTCTGATGAGTGAAGCACATCAAGCAATTTCTCATTTACAATCCGTCTCAATTACTTGTTAACACCTCTGACAATACCGATTCTGCAAGCTATTCAGTCTTTTCATTCCATGTAAATTGTCTCGATATTAATA  >  NC_000913/3360651‑3360894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A