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 F1 I2 R1	12	27.9	1984062	98.2%	1948348	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,737,118	IS1 (+) +8 bp	intergenic (+235/‑29)	bamD → / → raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1978503 =	NA (NA)	22 (0.660)	18/160	0.9	100%	noncoding (768/768 nt)	IS1	repeat region
*	?	NC_000913	2737118 =	0 (0.000)	22 (0.660)	18/160	0.9	100%	intergenic (+235/‑36)	bamD/raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor
*	?	NC_000913	= 1979270	NA (NA)	21 (0.630)	20/160	0.7	100%	noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	= 2737125	0 (0.000)	21 (0.630)	20/160	0.7	100%	intergenic (+242/‑29)	bamD/raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978581‑1978503

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  >  NC_000913/2737118‑2737194

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGA                                                                             <  1:175539/81‑1

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                              <  1:175540/80‑1

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                              <  1:175538/80‑1

 AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGA                                                                             >  1:175566/1‑80

      GGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCAC                                                                       <  2:789056/81‑1

            GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGAC                                                                 <  1:48956/81‑1

                CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGG                                                               <  1:3357/79‑1

                      AAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAA                                                       <  1:3368/81‑1

                              CGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAA                                                >  2:445490/1‑80

                               GGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAA                                               <  1:45176/80‑1

                                 GCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATT                                            <  2:45174/81‑1

                                  CATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTT                                           <  2:51188/81‑1

                                       TCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGA                                       >  2:445493/1‑80

                                              ATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAAC                               <  2:319545/81‑1

                                                AAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACAT                             >  2:445501/1‑81

                                                   ACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTAC                          <  2:51187/81‑1

                                                         TCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCA                     <  2:651180/80‑1

                                                                  TGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGG            >  1:445494/1‑80

                                                                      GTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATT       <  2:3348/81‑1

                                                                      GTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAAT        >  1:445492/1‑80

                                                                         ATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTAC     <  2:651178/80‑1

                                                                           TACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  >  2:445503/1‑81

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978581‑1978503

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  >  NC_000913/2737118‑2737194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A