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 I229 R1	214	17.4	943020	97.5%	919444	87.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	386,045	T→C	pseudogene (339/1527 nt)	BW25113_RS01915 →	outer membrane autotransporter barrel domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	386,045	0	T	C	100.0%	101.0 / NA	32	pseudogene (339/1527 nt)	BW25113_RS01915	outer membrane autotransporter barrel domain‑containing protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/16); total (16/16)

CACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTAC  >  NZ_CP009273/385961‑386126

cACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAt                                                                              >  1:115342/1‑90 (MQ=255)

 aCGATCTCAACCTATTATTTGAACCATGATTATGCAGGCAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:136220/90‑1 (MQ=255)

 aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:156968/90‑1 (MQ=255)

 aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:321811/90‑1 (MQ=255)

 aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:334522/90‑1 (MQ=255)

             tattatTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctg                                                                 >  1:89380/1‑90 (MQ=255)

              attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:260248/1‑90 (MQ=255)

              attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:44408/1‑90 (MQ=255)

              attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:12380/1‑90 (MQ=255)

                   ttGAACCATGATTATGCAGACAGTACTGCAAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                           <  1:406771/90‑1 (MQ=255)

                     gAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCgg                                                         >  1:218691/1‑90 (MQ=255)

                                aTGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATc                                              <  1:433858/90‑1 (MQ=255)

                                    aGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGttt                                          >  2:435459/1‑90 (MQ=255)

                                     gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGtttt                                         >  1:462072/1‑90 (MQ=255)

                                     gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCCATTACGTCTATGCTGCCTGGCGGTTTTTATGATCGtttt                                         >  2:194021/1‑90 (MQ=255)

                                         gTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTTTGCCGCCTGGCGGTTATTATGGTCGTTTTGAtt                                     >  2:300751/1‑89 (MQ=255)

                                              gCTAATCAGCTTGATATCAGTAGTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  2:362105/90‑1 (MQ=255)

                                              gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:308208/90‑1 (MQ=255)

                                              gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:143439/90‑1 (MQ=255)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             >  1:275480/1‑40 (MQ=39)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  2:275480/40‑1 (MQ=39)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:443705/85‑1 (MQ=255)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                >  2:443705/1‑85 (MQ=255)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaa                           <  1:417945/90‑1 (MQ=255)

                                                   tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTAATTATGATCGTTTTGATGCAGATGGtaa                           >  1:81180/1‑90 (MQ=255)

                                                      gCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaataa                        >  1:252477/1‑90 (MQ=255)

                                                             atCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGt                 <  2:313560/90‑1 (MQ=255)

                                                                aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGa              >  2:324742/1‑90 (MQ=255)

                                                                    aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          <  2:218691/90‑1 (MQ=255)

                                                                    aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          <  2:470202/90‑1 (MQ=255)

                                                                    aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          >  1:297248/1‑90 (MQ=255)

                                                                            aTTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTac  <  2:229958/90‑1 (MQ=255)

CACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTAC  >  NZ_CP009273/385961‑386126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATG  >  NZ_CP009273/385951‑386118

CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAT                                                                      <  SRR3722113.409898/100‑1 (MQ=60)

CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAT                                                                      >  SRR3722113.116342/1‑100 (MQ=60)

           ACGATCTCAACCTATTATTTGAACCATGATTATGCAGGCAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                           <  SRR3722113.137360/100‑1 (MQ=60)

           ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                           <  SRR3722113.324990/100‑1 (MQ=60)

           ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                           <  SRR3722113.337906/100‑1 (MQ=60)

           ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                           <  SRR3722113.158269/100‑1 (MQ=60)

             GATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTG                                                         >  SRR3722113.90186/1‑100 (MQ=60)

                     CCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGG                                                 >  SRR3722113.220440/1‑100 (MQ=60)

                             TTGAACCATGATTATGCAGACAGTACTGCAAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATG                                         <  SRR3722113.411044/100‑1 (MQ=60)

                                     TGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTT                                 >  SRR3722113.466957/1‑100 (MQ=60)

                                          ATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGC                            <  SRR3722113.438458/100‑1 (MQ=60)

                                                   GTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCctgtctcttatacacatctccgagcccacgagactaaggc                   >  SRR3722113.277904/1‑60 (MQ=60)

                                                   GTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTAATTATGATCGTTTTGATGCAGATGGTAA                   >  SRR3722113.81892/1‑100 (MQ=60)

                                                      CTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAA                >  SRR3722113.254665/1‑100 (MQ=60)

                                                        GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC              <  SRR3722113.311185/100‑1 (MQ=60)

                                                        GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC              <  SRR3722113.144622/100‑1 (MQ=60)

                                                        GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC              <  SRR3722113.448401/100‑1 (MQ=60)

                                                             TCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGT         <  SRR3722113.422360/100‑1 (MQ=60)

                                                                    GATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATG  >  SRR3722113.300045/1‑100 (MQ=60)

CCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATG  >  NZ_CP009273/385951‑386118

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`