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 I214 R1	12	15.1	924212	96.1%	888167	85.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	427,415	Δ2 bp	coding (54‑55/885 nt)	tsx ←	nucleoside‑specific channel‑forming protein Tsx

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	427,415	0	T	.	100.0%	50.2 / NA	12	coding (55/885 nt)	tsx	nucleoside‑specific channel‑forming protein Tsx
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (5/7); total (5/7)
*	NZ_CP009273	427,416	0	A	.	100.0%	50.2 / NA	12	coding (54/885 nt)	tsx	nucleoside‑specific channel‑forming protein Tsx
Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (5/7); total (5/7)

CCGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAGTAAAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATCC  >  NZ_CP009273/427342‑427493

||

ccGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAgcgc                                                              >  2:130620/1‑90 (MQ=255)

 cGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGcc                                                             <  1:139501/90‑1 (MQ=255)

 cGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGcc                                                             <  2:343356/90‑1 (MQ=255)

      aCGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTAc                                                        >  1:226434/1‑90 (MQ=255)

        gTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCg                                                      >  2:414580/1‑90 (MQ=255)

                                     gATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCata                         <  1:10658/90‑1 (MQ=255)

                                         cTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCAtatgta                     >  1:144511/1‑90 (MQ=255)

                                               tttGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCAc               <  1:130620/90‑1 (MQ=255)

                                               tttGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCAc               <  1:206715/90‑1 (MQ=255)

                                               tttGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCAc               <  1:51244/90‑1 (MQ=255)

                                                        ttCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGaaa      <  2:213296/90‑1 (MQ=255)

                                                            gCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATcc  >  1:221420/1‑90 (MQ=255)

||

CCGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAGTAAAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATCC  >  NZ_CP009273/427342‑427493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `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

GCTTCCGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAGTAAAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATCC  >  NZ_CP009273/427338‑427493

GCTTCCGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTAC                                                        >  SRR3722097.229096/1‑100 (MQ=60)

     CGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCAC                                                   <  SRR3722097.141131/100‑1 (MQ=60)

                                   CGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTA                     >  SRR3722097.146196/1‑100 (MQ=60)

                                         GATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCAC               <  SRR3722097.10786/100‑1 (MQ=60)

                                                   TTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAA     <  SRR3722097.132169/100‑1 (MQ=60)

                                                   TTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAA     <  SRR3722097.209046/100‑1 (MQ=60)

                                                   TTTGTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAA     <  SRR3722097.51830/100‑1 (MQ=60)

                                                      GTCGTTTTCAGCTGCGTTGACAG‑‑AAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATCC  >  SRR3722097.223984/1‑100 (MQ=60)

GCTTCCGACAACGTTAACGCTCTGGTGCCACCAGTCGGAAAGATACTGCGGTTTGTCGTTTTCAGCTGCGTTGACAGTAAAAGACGAAGAGAGCGCCAGTACCGCACCGGCTGCCAGTAATGTTTTTTTCATATGTATGCCACTGTTTGAAAATCC  >  NZ_CP009273/427338‑427493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`