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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,568,417	C→T	G35R (GGG→AGG)	mdtM ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,568,417	0	C	T	100.0%	168.5 / NA	48	G35R (GGG→AGG)	mdtM	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (24/24); total (24/24)

ACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAC  >  NC_000913/4568281‑4568551

aCCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAg                                                                                                                                      >  1:978329/1‑139 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAGATCACGTACCACATTAATGATCCTAGGCTg                                                                                                                                  >  1:487124/1‑139 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    <  1:197176/137‑1 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    >  2:197176/1‑137 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTg                                                                                                                                  >  1:852763/1‑139 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTg                                                                                                                                  >  1:389897/1‑139 (MQ=255)

    gCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTg                                                                                                                                  >  1:487123/1‑139 (MQ=255)

            ccAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGAt                                                                                                                          <  2:1048582/139‑1 (MQ=255)

            ccAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGAt                                                                                                                          <  2:468745/139‑1 (MQ=255)

                 tCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTc                                                                                                                     <  1:876333/139‑1 (MQ=255)

                        gAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAACAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGAt                                                                                                              <  2:899346/139‑1 (MQ=255)

                         aaaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATa                                                                                                             <  2:916313/139‑1 (MQ=255)

                          aaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATAc                                                                                                            <  2:852763/139‑1 (MQ=255)

                             cGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgca                                                                                                         >  1:882473/1‑139 (MQ=255)

                                ccccAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgcagca                                                                                                      <  2:389897/139‑1 (MQ=255)

                                   cagcagCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAg                                                                                                   <  2:94382/139‑1 (MQ=255)

                                   cagcagCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAg                                                                                                   <  2:1056274/139‑1 (MQ=255)

                                         ccACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    <  1:567522/100‑1 (MQ=255)

                                         ccACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    >  2:567522/1‑100 (MQ=255)

                                                   gCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    >  2:198893/1‑90 (MQ=255)

                                                   gCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                    <  1:198893/90‑1 (MQ=255)

                                                      aTACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCa                                                                                <  2:300252/139‑1 (MQ=255)

                                                       tACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCAt                                                                               >  1:447987/1‑139 (MQ=255)

                                                             cAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGaa                                                                         >  2:454150/1‑139 (MQ=255)

                                                                   gATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAg                                                                   <  1:281366/139‑1 (MQ=255)

                                                                        agaCTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgcag                                                                                                        >  2:884031/1‑97 (MQ=255)

                                                                        agaCTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgcag                                                                                                        <  1:884031/97‑1 (MQ=255)

                                                                          aCTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTggcg                                                            >  2:573510/1‑139 (MQ=255)

                                                                            tGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTggcggc                                                          >  1:203480/1‑139 (MQ=255)

                                                                              aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAgg                                                                                                                                     >  2:1072993/1‑62 (MQ=255)

                                                                              aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAgg                                                                                                                                     <  1:1072993/62‑1 (MQ=255)

                                                                              aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCAt                                                        >  1:718634/1‑139 (MQ=255)

                                                                               cGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGACATg                                                       <  1:773269/139‑1 (MQ=255)

                                                                                  cagcagGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCg                                                    <  2:946691/139‑1 (MQ=255)

                                                                                    gcagGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAGCGCCATCGGGAAAAACAGCGTGGCGGCATGGCggg                                                  >  2:671085/1‑139 (MQ=255)

                                                                                    gcagGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCggg                                                  >  2:305674/1‑139 (MQ=255)

                                                                                               aCTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCa                                                                                <  1:5141/98‑1 (MQ=255)

                                                                                               aCTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCa                                                                                >  2:5141/1‑98 (MQ=255)

                                                                                                cTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTg                                      <  2:882473/139‑1 (MQ=255)

                                                                                                         gCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaa                             >  1:409523/1‑139 (MQ=255)

                                                                                                                    aCGTACCACATTAATGATCCTAGGCTGGATCAGATCCGTCGACACATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGAAAAAAAACGTGGCATAACAAACAACTTCTTg                  >  1:783964/1‑139 (MQ=255)

                                                                                                                         ccACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgcagca                                                                                                      <  1:392673/50‑1 (MQ=255)

                                                                                                                         ccACATTAATGATCCTAGGCTGGATCAGATCCGTCGACAGATACgcagca                                                                                                      >  2:392673/1‑50 (MQ=255)

                                                                                                                                 aTGATCCTAGGCTGGATCAGCTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAAcccc     >  1:126008/1‑139 (MQ=255)

                                                                                                                                  tGATCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGt                 >  2:97397/1‑126 (MQ=255)

                                                                                                                                  tGATCCTAGGCTGGATCAGAACCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGt                 <  1:97397/126‑1 (MQ=255)

                                                                                                                                    aTCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCAt                                  <  2:246653/107‑1 (MQ=255)

                                                                                                                                    aTCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCAt                                  >  1:246653/1‑107 (MQ=255)

                                                                                                                                    aTCCTAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAc  <  2:203480/139‑1 (MQ=255)

ACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAC  >  NC_000913/4568281‑4568551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A