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 F3 I95 R1	196	14.2	808436	96.0%	776098	85.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,543,103	A→G	E129G (GAA→GGA)	uxuB →	fructuronate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,543,103	0	A	G	92.9%	35.7 / ‑3.0	14	E129G (GAA→GGA)	uxuB	fructuronate reductase
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (5/8); total (5/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01

GCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGA  >  NZ_CP009273/4543017‑4543183

gcTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGgaaa                                                                               <  2:140440/90‑1 (MQ=255)

  tGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAg                                                                             <  1:168160/90‑1 (MQ=255)

  tGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAg                                                                             <  2:387749/90‑1 (MQ=255)

              tCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTg                                                                 <  2:244560/90‑1 (MQ=255)

                           aGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg                                                    <  2:93754/90‑1 (MQ=255)

                                   tcAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTgg                                            <  2:312407/90‑1 (MQ=255)

                                    cAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGa                                           >  2:105927/1‑90 (MQ=255)

                                      aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc                                         >  1:400909/1‑90 (MQ=255)

                                                  gTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGc                             <  2:400909/90‑1 (MQ=255)

                                                              cGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGc                             <  1:355003/78‑1 (MQ=255)

                                                              cGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGc                             >  2:355003/1‑78 (MQ=255)

                                                                aTTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCGAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGAt               <  1:95927/90‑1 (MQ=255)

                                                                       ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGc                                                      <  1:207031/44‑1 (MQ=255)

                                                                       ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGc                                                      >  2:207031/1‑44 (MQ=255)

                                                                             cGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGa  >  1:390682/1‑90 (MQ=255)

GCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGA  >  NZ_CP009273/4543017‑4543183

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

AAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGA  >  NZ_CP009273/4543009‑4543183

AAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAG                                                                             <  SRR3722235.139031/100‑1 (MQ=60)

          TGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGC                                                                   <  SRR3722235.170093/100‑1 (MQ=60)

                                 ttgtctcgtgggctcggagatgtgtataagagacaGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGG                                            <  SRR3722235.209580/65‑1 (MQ=60)

                                    GGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATC                                         >  SRR3722235.406692/1‑100 (MQ=60)

                                                          agCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCA                   <  SRR3722235.360113/98‑1 (MQ=60)

                                                                        ATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCGAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACC     <  SRR3722235.97049/100‑1 (MQ=60)

                                                                           GTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGA  >  SRR3722235.396310/1‑100 (MQ=60)

AAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGA  >  NZ_CP009273/4543009‑4543183

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `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: `‑`