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
A2 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	592,602	C→T	Q6* (CAA→TAA)	cusF →	Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	592,602	0	C	T	100.0%	128.5 / NA	32	Q6* (CAA→TAA)	cusF	Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (13/19); total (13/19)

CGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTA  >  NZ_CP009273/592468‑592725

cgtctgcgtTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAg                                                                                                                          <  2:15452/138‑1 (MQ=255)

 gtctgcgtTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTc                                                                                                                        <  1:566454/139‑1 (MQ=255)

           gCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTc                                                                                                               <  2:343352/138‑1 (MQ=255)

            cTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAg                                                                                                             <  1:541258/139‑1 (MQ=255)

               aCCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGt                                                                                                            <  2:56110/137‑1 (MQ=255)

               aCCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGt                                                                                                            <  1:381508/137‑1 (MQ=255)

                    aGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTa                                                                                                     <  2:364579/139‑1 (MQ=255)

                     gTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAc                                                                                                    >  1:448039/1‑139 (MQ=255)

                           tacttaTGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTAt                                                                                              >  1:133047/1‑139 (MQ=255)

                            acttaTGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTa                                                                                               <  2:545320/137‑1 (MQ=255)

                                aTGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCt                                                                                         >  2:240963/1‑139 (MQ=255)

                                aTGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCt                                                                                         >  1:576390/1‑139 (MQ=255)

                                  gTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCtt                                                                                        >  1:156327/1‑138 (MQ=255)

                                       cTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGc                                                                                  >  1:260922/1‑139 (MQ=255)

                                        tCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGcc                                                                                 >  1:256060/1‑139 (MQ=255)

                                             gggATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAgg                                                                             <  2:61296/138‑1 (MQ=255)

                                                   cACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACg                                                                       <  2:133047/138‑1 (MQ=255)

                                                    aCTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGc                                                                                                                      <  2:334349/90‑1 (MQ=255)

                                                    aCTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGc                                                                                                                      >  1:334349/1‑90 (MQ=255)

                                                    aCTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGaa                                                                     >  2:129769/1‑139 (MQ=255)

                                                            gTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatcatca                                                             >  1:444567/1‑139 (MQ=255)

                                                                    ccTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAAcc                                                      <  2:156327/138‑1 (MQ=255)

                                                                        cAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAg                                                 <  2:444567/139‑1 (MQ=255)

                                                                           cTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGa                                              <  2:260922/139‑1 (MQ=255)

                                                                               aaTTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGca                                          <  1:192230/139‑1 (MQ=255)

                                                                                      tAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACca                                    >  2:518273/1‑138 (MQ=255)

                                                                                                   ttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcat                                                                  >  1:575046/1‑95 (MQ=255)

                                                                                                   ttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcat                                                                  <  2:575046/95‑1 (MQ=255)

                                                                                                          cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGc               <  1:518273/139‑1 (MQ=255)

                                                                                                                agaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTa         <  1:520119/139‑1 (MQ=255)

                                                                                                                  aaTAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTa         >  1:131385/1‑137 (MQ=255)

                                                                                                                       aTGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTa  <  2:131385/139‑1 (MQ=255)

CGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTA  >  NZ_CP009273/592468‑592725

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTATCGA  >  NZ_CP009273/592452‑592729

agtctagtacggtctcgtgggctcggagatgtgtataagagacagCTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGT                                                                                                                                 <  SRR3722139.461345/106‑1 (MQ=60)

     agtacggtctcgtgggctcggagatgtgtataagagacagCTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGT                                                                                                                                 <  SRR3722139.124921/106‑1 (MQ=60)

                CGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAG                                                                                                                 <  SRR3722139.572950/151‑1 (MQ=60)

                          CGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACC                                                                                                       >  SRR3722139.453288/1‑151 (MQ=60)

                           GCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCG                                                                                                      <  SRR3722139.547499/151‑1 (MQ=60)

                              CACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGT                                                                                                     <  SRR3722139.386061/149‑1 (MQ=60)

                                CCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATT                                                                                                 >  SRR3722139.134666/1‑151 (MQ=60)

                                     GTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTT                                                                                            >  SRR3722139.582968/1‑151 (MQ=60)

                                       CACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTT                                                                                           >  SRR3722139.158238/1‑150 (MQ=60)

                                            GCTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCC                                                                                     >  SRR3722139.264201/1‑151 (MQ=60)

                                             CTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCC                                                                                    >  SRR3722139.259281/1‑151 (MQ=60)

                                                         CCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCctgtctcttatacacatctccgagcccacgagaccgtac                                                                        >  SRR3722139.338438/1‑112 (MQ=60)

                                                                 TTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCAT                                                                >  SRR3722139.449783/1‑151 (MQ=60)

                                                                                              GAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGT                                   <  SRR3722139.194606/151‑1 (MQ=60)

                                                                                                        GAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCtgtctcttatacacatctccgagcccacgagac                         >  SRR3722139.581617/1‑118 (MQ=60)

                                                                                                                       CTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAA            >  SRR3722139.132993/1‑149 (MQ=60)

                                                                                                                         CCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGG        <  SRR3722139.524223/151‑1 (MQ=60)

                                                                                                                               GAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTATCGA  <  SRR3722139.526118/151‑1 (MQ=60)

CAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAGCGCCACTGGCGTGGTAAAGGGTATCGA  >  NZ_CP009273/592452‑592729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`