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
A3 F44 I0 R1	30	22.2	989614	86.8%	858984	142.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	568,268	IS1 (–) +9 bp	100%	intergenic (+21/‑39)	renD → / → emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	19796 =	NA (NA)	10 (0.410)	9/262	NT	100%	noncoding (768/768 nt)	IS1	repeat region
*	?	NC_000913	= 568276	0 (0.000)	10 (0.410)	9/262	NT	100%	intergenic (+29/‑39)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
*	?	NC_000913	= 258675	NA (NA)	22 (0.900)	21/264	NT	100%	noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	568268 =	0 (0.000)	22 (0.900)	21/264	NT	100%	intergenic (+21/‑47)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/19936‑19796

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTA  <  NC_000913/568276‑568172

CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCATATTCGGTGTAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTA                                                                                                         <  1:269057/143‑1

  GCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTAATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGACATTACCTACA                                                                                                       >  1:201547/1‑143

         CTGAATCTGGTGGAGCACCTGGCGCGGCTGGGACGGAAGTTGCTGTCGTTCTCAAAATCGGTGGAGCTGCGTGACAAAGGCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAA                                                                                                <  1:310832/143‑1

          TGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAGACACTATCAATAAGTTGGAGTCATTACCTACAGTCTGAAC                                                                                               >  2:351016/1‑143

                          ctTGGCACGGCTCGGACGGACGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGTGCATTATCTGAACAGAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTC                                                                               <  2:325582/141‑1

                          CCTGGCACGGCTGGGACGGAAGGCGCTGTCGGTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTC                                                                               <  2:27946/143‑1

                           CTGGCACGGTTTTGACGGAAGTCGCTGTCGTTCTCAAAATCGGCGGCGCTGAACAACAGAGTCGTCGGACATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCA                                                                              <  1:190039/143‑1

                               CACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACACAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCAT                                                                          >  1:303180/1‑143

                                                                              CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGCTGGAGTCATTACCTACAGTATAAACTCAACACACCTGTTACATCATTGTGTTCCCATTGATGTTCTTTTATATACACTCAATACCCGTTTCAT                           >  1:43892/1‑143

                                                                                    AAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATGTACCCTCGATACCGGTTTCATCGCacc                     >  2:216580/1‑140

                                                                                          ATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTAAACTCAACTCACCTGTTTCATCATTGTGTTCCAATTAATGTTCTTTTATATACCCTCAATCCCCGTTTAATCCCGGCACTCac               >  2:455899/1‑141

                                                                                                       TGAACATAAAACACTATCAATAAGTTGGAGGCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGGGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTA  >  1:439088/1‑143

CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/19936‑19796

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTA  <  NC_000913/568276‑568172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `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