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
A5 F28 I1 R1	139	58.0	1973578	98.9%	1951868	138.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,278,738	C→T	T341T (ACG→ACA)	bcr ←	multidrug efflux pump Bcr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,278,738	0	C	T	100.0%	88.6 / NA	26	T341T (ACG→ACA)	bcr	multidrug efflux pump Bcr
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (24/2); total (24/2)

AGAAGAGAATGGAGCTGGTTGCGCAGAATGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAGCGCACTGA  >  NC_000913/2278602‑2278868

agaagaGAATGGAGCTGGTTGCGCAGAATGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGtt                                                                                                                                 >  1:667558/1‑140 (MQ=255)

 gaagaGAATGGAGCTGGTTGCGCAGAATGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTc                                                                                                                                >  1:277320/1‑140 (MQ=255)

       aaTGGGGCTGGTTGCGAAGAATGCAATTGACCAAATCACCGGCCATGCAGAGTAAAAGGTCGCAAGAGAAAGCAATGCCCCAACATTTGCCCCTATGCAAAAAGGGAAGGTC‑CCTGCCAGCGAAGATGCTGTTCCCGCCa                                                                                                                          <  2:611524/140‑1 (MQ=255)

            aGCTGGTTGCGCAGAATGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATgg                                                                                                                     >  1:532064/1‑140 (MQ=255)

                 gTTGCGAAGAATGCAATTAACAAAACCATCGGCCATGCAGAGTAAAAGGTCGCAAGAAAAAGCAATGCCCCAACAATTCCCCCTATGCCAAAAGGGAAGTTC‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGaaa                                                                                                                <  2:931905/140‑1 (MQ=255)

                           aTGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGa                                                                                                      >  1:278725/1‑140 (MQ=255)

                                      cagaccatcGCCCATGCAGAGTAAAAGGTCGAAAGAGAAAGCAATGCGCCAACAATTCCCCCTATGCCAAAACGGAAGGTC‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCAt                                                                                           <  2:307417/135‑1 (MQ=255)

                                      aaaaTCATCGGCCATGCAGAGTAAAAGGTCGAAAGAGAAAGCAATGCCCAAACATTTCCCCCTATGCAAAAAGGGAAGGTC‑CCTGCCAGCGAAGATGTTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCAt                                                                                           <  2:278725/139‑1 (MQ=255)

                                          tctgcGGCCATGAAGAGTTAAGGGGCGAAAGAAAAAGCAATGCCCAAAAATTTCCCCCTAGCCAAAAACGGAAGGTC‑CCGGCCAGCAAAGATGCTGTCCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCa                                                                                       <  2:667558/136‑1 (MQ=255)

                                          agacgggCCATGCAGATTAAAGGGTCGAAAGAAAAAGCAATGCGCCAACAATCGCCCCTATCCAAAAAGGGAAGTTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCa                                                                                       <  2:301327/135‑1 (MQ=255)

                                             tcGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTg                                                                                    >  1:981618/1‑140 (MQ=255)

                                               ggCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGa                                                                                  >  2:437208/1‑140 (MQ=255)

                                                gCCATGCAGAGTAAAAGGCCGAAAGAAAAAGAAAGGCCCAAACATTTCCCCCTATCCAAAAGGGGAAGTTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGAt                                                                                 <  2:868530/140‑1 (MQ=255)

                                                   aTGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGACGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGac                                                                              >  2:512377/1‑140 (MQ=255)

                                                    tGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATgctg                                                                             >  1:307417/1‑137 (MQ=255)

                                                           ttAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACAcctgtct                                                                      >  1:301327/1‑135 (MQ=255)

                                                           ttAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGa                                                                      >  1:278987/1‑140 (MQ=255)

                                                               aGGCCGAAAGAAAAAGCAATGCGCAAACAATTCCCCCTATCCCAAAGGGGAAGGTT‑CCTGCCAGCAAAGATGCTGTCCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACg                                                                  <  2:157283/140‑1 (MQ=255)

                                                                ggacgaaaGAGAAAGAAAGGCGCAAAAACTCGCCCCTATGCAAAAAGGGAGGGTC‑CCTGCCAGCAAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGc                                                                 <  2:769831/134‑1 (MQ=255)

                                                                   cGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGc                                                              >  2:141183/1‑140 (MQ=255)

                                                                   cGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTCCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGc                                                              >  2:779072/1‑140 (MQ=255)

                                                                     cAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGccc                                                            >  1:345392/1‑140 (MQ=255)

                                                                        gaaaaaGCAAGGCCCCAACATTTCCCCCTA‑CCCAAAAAGGGAGGTTCCCGGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCcaca                                                         <  2:278987/137‑1 (MQ=255)

                                                                               aaaggccccAAAAATTGCCCCTATCCCAAAGCGGAAGTTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAAcgccg                                                  <  2:532064/133‑1 (MQ=255)

                                                                                  tGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCaa                                               >  2:770267/1‑140 (MQ=255)

                                                                                    cgcCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAAcc                                             >  2:140713/1‑139 (MQ=255)

                                                                                                ccccTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGcc                                           >  2:28843/1‑130 (MQ=255)

                                                                                                ccccTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGcc                                           <  1:28843/130‑1 (MQ=255)

                                                                                                   cTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGAc                              >  2:852375/1‑140 (MQ=255)

                                                                                                     aTGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCa                            >  2:33655/1‑140 (MQ=255)

                                                                                                          aaaaCGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATc                       <  1:852375/140‑1 (MQ=255)

                                                                                                            aaCGGAAGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATccc                     <  1:33655/140‑1 (MQ=255)

                                                                                                               ggAAGTTC‑CCTGCCAGCAAAGATGCTGTCCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagc                  <  2:847959/140‑1 (MQ=255)

                                                                                                                 aaGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccc                >  1:581307/1‑140 (MQ=255)

                                                                                                                 aaGGTT‑CCTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATAGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccc                >  1:860895/1‑140 (MQ=255)

                                                                                                                        ccTGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCcagcag          >  2:671061/1‑140 (MQ=255)

                                                                                                                         ctaccAGAGAGGAGGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCagcagc         <  2:345392/137‑1 (MQ=255)

                                                                                                                          tGCCAGCGAGGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAgcg        <  1:512377/140‑1 (MQ=255)

                                                                                                                          tGCCAGCGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAgcg        <  1:671061/140‑1 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccccag             <  2:134536/129‑1 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccccag             >  1:134536/1‑129 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccc                <  1:912766/126‑1 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATcccagccc                >  2:912766/1‑126 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAGCGCACtga  >  1:786496/1‑140 (MQ=255)

                                                                                                                                cGAAGATGCTGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAGCGCACtga  <  2:786496/140‑1 (MQ=255)

AGAAGAGAATGGAGCTGGTTGCGCAGAATGCAATTGACCAAATCATCGGCCATGCAGAGTTAAAGGTCGCAAGAGAAAGCAATGCGCCAACAATTGCCCCTATGCCAAAACGGAAGGTT‑CCTGCCAGCGAAGATGCCGTTCCCGCCATATGGGGAAACTCATCAAGAATGACCGCCATCGCATTGGATGACACCATCGACACGCAGCCCACAAACGCCGCAACGCCAACCACCAGCGACCAAAATCCCAGCCCCAGCAGCGCACTGA  >  NC_000913/2278602‑2278868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A