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 I207 R1	218	45.0	2482936	97.1%	2410930	86.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	476,525	A→G	intergenic (‑361/+185)	tomB ← / ← acrB	Hha toxicity modulator TomB/efflux RND transporter permease AcrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	476,525	0	A	G	100.0%	95.1 / NA	28	intergenic (‑361/+185)	tomB/acrB	Hha toxicity modulator TomB/efflux RND transporter permease AcrB
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/14); total (14/14)

AGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGG  >  NZ_CP009273/476439‑476607

aGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGgtta                                                                                 >  2:56154/1‑90 (MQ=255)

 ggATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGgttat                                                                                <  2:181109/90‑1 (MQ=255)

 ggATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGgttat                                                                                <  1:454073/90‑1 (MQ=255)

   aTTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGttatta                                                                              <  1:39465/90‑1 (MQ=255)

    ttGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTaa                                                                             >  1:1220339/1‑90 (MQ=255)

    ttGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTaa                                                                             >  2:44178/1‑90 (MQ=255)

     tGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTaaa                                                                            <  1:95822/90‑1 (MQ=255)

      gCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAAt                                                                           >  1:480206/1‑90 (MQ=255)

       ctctGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATc                                                                          <  1:233532/90‑1 (MQ=255)

           gAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTAtt                                                                      >  1:212574/1‑90 (MQ=255)

           gAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTAtt                                                                      <  1:601376/90‑1 (MQ=255)

                tGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAgcgc                                                                 <  2:882603/90‑1 (MQ=255)

                tGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAgcgc                                                                 <  1:289416/90‑1 (MQ=255)

                     taataaCCGAGGAATGAATAAAGGATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACtt                                                            >  1:1216729/1‑90 (MQ=255)

                     taataaCCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACtt                                                            <  2:1232567/90‑1 (MQ=255)

                     taataaCCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACtt                                                            <  2:1113656/90‑1 (MQ=255)

                            cGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATaa                                                     >  2:601928/1‑90 (MQ=255)

                             gAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATaaa                                                    >  1:907723/1‑90 (MQ=255)

                             gAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATaaa                                                    >  1:122213/1‑90 (MQ=255)

                              aGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAAt                                                   <  2:122213/90‑1 (MQ=255)

                                  atgaatAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATtaac                                               <  1:60239/90‑1 (MQ=255)

                                         aaGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAAt                                        >  2:541814/1‑90 (MQ=255)

                                              ttACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTa                                   >  1:667720/1‑90 (MQ=255)

                                              ttACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTa                                   >  2:255743/1‑90 (MQ=255)

                                                      aataatTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTAt                           <  2:234352/90‑1 (MQ=255)

                                                                  tAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCg               <  2:541839/90‑1 (MQ=255)

                                                                   aGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGt              >  2:1006469/1‑90 (MQ=255)

                                                                       tctAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGtt          <  2:907723/90‑1 (MQ=255)

                                                                             tGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACt    <  1:541814/90‑1 (MQ=255)

                                                                              gATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTg   >  1:1219499/1‑90 (MQ=255)

                                                                               aTTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTgg  >  1:114943/1‑90 (MQ=255)

AGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGG  >  NZ_CP009273/476439‑476607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 35 ≤` `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

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTA  >  NZ_CP009273/476426‑476615

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGG                                                                                            <  SRR3722089.940053/100‑1 (MQ=60)

       AATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAA                                                                                     <  SRR3722089.1151108/100‑1 (MQ=60)

       AATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAA                                                                                     >  SRR3722089.1238898/1‑100 (MQ=60)

         TACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAAT                                                                                   >  SRR3722089.485915/1‑100 (MQ=60)

           CCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCT                                                                                 <  SRR3722089.627834/100‑1 (MQ=60)

              GGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATT                                                                              <  SRR3722089.459512/100‑1 (MQ=60)

              GGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATT                                                                              >  SRR3722089.215256/1‑100 (MQ=60)

                ATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAG                                                                            <  SRR3722089.39957/100‑1 (MQ=60)

                  TGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCG                                                                          <  SRR3722089.97013/100‑1 (MQ=60)

                    CTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCT                                                                        <  SRR3722089.236498/100‑1 (MQ=60)

                        GAATATGACGTAATAACCGAGGAATGAATAAAGGATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTT                                                                    >  SRR3722089.1235238/1‑100 (MQ=60)

                        GAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTT                                                                    <  SRR3722089.608781/100‑1 (MQ=60)

                             nnnnnnnnnnnnnnnnnnnnGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATAT                                                               <  SRR3722089.789644/80‑1 (MQ=60)

                             ggcgaccaccgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagGATTATGGGTTATTAAATCTATTAGCGCTACTTAATAT                                                               <  SRR3722089.1008904/38‑1 (MQ=60)

                             TGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATAT                                                               <  SRR3722089.293119/100‑1 (MQ=60)

                                CGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAA                                                            >  SRR3722089.123703/1‑100 (MQ=60)

                                CGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAA                                                            >  SRR3722089.920920/1‑100 (MQ=60)

                                               ATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAG                                             <  SRR3722089.60979/100‑1 (MQ=60)

                                                 GAATAAAGGATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTA                                           >  SRR3722089.676358/1‑100 (MQ=60)

                                                                                 GCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTG           >  SRR3722089.1238050/1‑100 (MQ=60)

                                                                                  CCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGG          >  SRR3722089.116348/1‑100 (MQ=60)

                                                                                          TGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTA  <  SRR3722089.548122/100‑1 (MQ=60)

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTA  >  NZ_CP009273/476426‑476615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`