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
A1 F2 I194 R1	197	32.2	1845014	95.2%	1756453	85.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,576,634	A→G	R79R (CGA→CGG)	BW25113_RS17825 →	YrhA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,576,634	0	A	G	100.0%	119.7 / NA	34	R79R (CGA→CGG)	BW25113_RS17825	YrhA family protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/12); total (22/12)

GAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCAT  >  NZ_CP009273/3576551‑3576717

gAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTAttt                                                                               >  1:696725/1‑90 (MQ=255)

gAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTAttt                                                                               >  2:114126/1‑90 (MQ=255)

 aaGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTa                                                                              <  1:483535/90‑1 (MQ=255)

   gTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGc                                                                            >  2:757595/1‑90 (MQ=255)

     tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAGTGGATTACGGTTATTTAGCct                                                                          >  1:257646/1‑90 (MQ=255)

      aGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCctc                                                                         >  2:86448/1‑90 (MQ=255)

       gTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCctct                                                                        >  1:437689/1‑90 (MQ=255)

         aTTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCg                                                                      <  2:656114/90‑1 (MQ=255)

         aTTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCg                                                                      <  2:278690/90‑1 (MQ=255)

                 tAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGa                                                              >  1:199799/1‑90 (MQ=255)

                      aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                         >  1:376178/1‑90 (MQ=255)

                      aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                         >  2:368335/1‑90 (MQ=255)

                          aCCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGt                                                     >  2:588599/1‑90 (MQ=255)

                              gATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTaaa                                                 >  1:744570/1‑90 (MQ=255)

                              gATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTaaa                                                 >  1:864634/1‑90 (MQ=255)

                                    cTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCtt                                           >  2:909185/1‑90 (MQ=255)

                                    cTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCtt                                           >  1:242342/1‑90 (MQ=255)

                                    cTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCtt                                           >  1:321981/1‑90 (MQ=255)

                                       aCTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCttttt                                        <  2:549726/90‑1 (MQ=255)

                                         ttttttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGc                                      <  2:515313/90‑1 (MQ=255)

                                                 gagCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATg                              <  1:187616/90‑1 (MQ=255)

                                                 gagCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATg                              <  1:453702/90‑1 (MQ=255)

                                                  agCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGa                             >  2:262009/1‑90 (MQ=255)

                                                    cAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAAt                           <  1:748243/90‑1 (MQ=255)

                                                      atggagggATTCGAGGTTATTGGGTAACGGTTATTTAGCCTCACGATTCCAGAACCTTCGGTTAAAAACCTTTTTGCCGTATATCAAttt                         >  2:378781/1‑90 (MQ=255)

                                                         gatggatTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAATTAAAAACCTTTTTGCCGTAAATGAATTTtat                      <  2:321981/90‑1 (MQ=255)

                                                             gatTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGaa                  >  2:187613/1‑90 (MQ=255)

                                                              atTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGaaa                 >  1:38941/1‑90 (MQ=255)

                                                                tCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAaata               >  2:181155/1‑90 (MQ=255)

                                                                       tAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAAtgatga        <  1:806223/90‑1 (MQ=255)

                                                                       tAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAAtgatga        >  2:732545/1‑90 (MQ=255)

                                                                        aaTGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATgatgat       <  2:398968/90‑1 (MQ=255)

                                                                         aTGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGAtt      <  2:333770/90‑1 (MQ=255)

                                                                             aTTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCAt  >  2:646581/1‑90 (MQ=255)

GAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCAT  >  NZ_CP009273/3576551‑3576717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAA  >  NZ_CP009273/3576536‑3576733

GAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGT                                                                                                    >  SRR3722072.362931/1‑100 (MQ=60)

GAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGT                                                                                                    >  SRR3722072.667824/1‑100 (MQ=60)

     GTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTT                                                                                               >  SRR3722072.709193/1‑100 (MQ=60)

          GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAGTGGATTACGGTTATTTAGCCT                                                                                          >  SRR3722072.262014/1‑100 (MQ=60)

            AATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCT                                                                                        >  SRR3722072.445671/1‑100 (MQ=60)

                AAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGAT                                                                                    <  SRR3722072.492293/100‑1 (MQ=60)

                   catacgagataatcggacgtctcgtgggctcggagatgtgtataagagacagGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCC                                                                                 <  SRR3722072.1162/48‑1 (MQ=60)

                      GTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGA                                                                              >  SRR3722072.203246/1‑100 (MQ=60)

                           CTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTT                                                                         >  SRR3722072.382886/1‑100 (MQ=60)

                                   GAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAA                                                                 >  SRR3722072.879548/1‑100 (MQ=60)

                                   GAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAA                                                                 >  SRR3722072.757742/1‑100 (MQ=60)

                                         ACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTT                                                           >  SRR3722072.246407/1‑100 (MQ=60)

                                         ACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTT                                                           >  SRR3722072.327608/1‑100 (MQ=60)

                                                                GAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAG                                    <  SRR3722072.190878/100‑1 (MQ=60)

                                                                GAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAG                                    <  SRR3722072.462006/100‑1 (MQ=60)

                                                                   CAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAA                                 <  SRR3722072.761473/100‑1 (MQ=60)

                                                                   CAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAA                                 >  SRR3722072.39642/1‑100 (MQ=60)

                                                                                      TAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAAC              <  SRR3722072.820282/100‑1 (MQ=60)

                                                                                          GGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTG          >  SRR3722072.665356/1‑100 (MQ=60)

                                                                                           GATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGA         >  SRR3722072.77676/1‑100 (MQ=60)

                                                                                                  GTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGActgtctcttatacacatctcctagc  >  SRR3722072.450875/1‑75 (MQ=60)

                                                                                                  GTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAA  >  SRR3722072.529204/1‑100 (MQ=60)

                                                                                                  GTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAA  <  SRR3722072.374881/100‑1 (MQ=60)

                                                                                                  GTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAA  >  SRR3722072.152776/1‑100 (MQ=60)

GAGAAGTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAA  >  NZ_CP009273/3576536‑3576733

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`