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 F34 I0 R1	41	39.6	1695432	90.3%	1530975	142.9

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	= 258675	NA (NA)	40 (0.920)	38/264	NT	100%	noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	568268 =	0 (0.000)	40 (0.920)	38/264	NT	100%	intergenic (+21/‑47)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
*	?	NC_000913	= 568276	0 (0.000)	32 (0.740)	27/262	NT	100%	intergenic (+29/‑39)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
*	?	NC_000913	= 1050545	NA (NA)	32 (0.740)	27/262	NT	100%	noncoding (768/768 nt)	IS1	repeat region

CGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258535‑258675

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGG  >  NC_000913/568268‑568401

CGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCGGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAGCACCATCAGACAGTAAATAAGTAAGTTGGGAGCAGCACCCA                                                                                                                                      >  1:279043/1‑143

  CTGATGTCCGGCGGTGCTTGTGCCGTTACGCACCACACCGTCAGTAGCTGAACAGGAGGGACCGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAA                                                                                                                                    <  2:558511/143‑1

   TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAC                                                                                                                                   >  1:502912/1‑143

      TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGGAGCTGAGCAGGAGGGACAGCTGATAGAAACCGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAGTCAGTAAGTTGGCAGCATCACCCAATCTGT                                                                                                                                <  2:218216/143‑1

       GTCCGGCGGTGCTCTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTA                                                                                                                               <  1:542800/143‑1

        TCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTCAGTTGGCAGCATCACCCAAACCGTAG                                                                                                                              >  2:123560/1‑143

          CGGCGCTGCATGTGCCGGTACGCCCCACCCCGTCACTAGCTGAACAGGAGCGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAACACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTA                                                                                                                            <  2:395535/143‑1

              GGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACATCAAAAACACCATCATCCACTACATCAGTAAGTTGGCAGCATCTCCCACACTGTAGTACAAT                                                                                                                        >  1:136395/1‑143

                  CTTTTGCCGTTACGCCCCCCCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTC                                                                                                                    <  2:459005/143‑1

                         CGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTT                                                                                                             <  2:235708/143‑1

                           TTACGCACCCGCCCGCCAGTAGCTGAACAGGAGCGACAGCTGCTAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCTTCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTG                                                                                                           <  1:799600/143‑1

                             ACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACATCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAA                                                                                                         <  2:424093/143‑1

                             ACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACCGTAGTACAATTCTCTCCAGTTTGAA                                                                                                         >  2:544907/1‑143

                             ACGCACCACCCCGTCAGGAGCTGAACAGGAGGGACAGCTGAGAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACCAAATCAGTAAGCTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAA                                                                                                         <  2:516929/143‑1

                                  CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGA                                                                                                    >  1:554695/1‑143

                                   CACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAATTCACCAGCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAA                                                                                                   >  1:757465/1‑143

                                       CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAA                                                                                               <  1:501091/143‑1

                                             ggAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAAGCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTATCCCGTTTGATCAGGAAAGAATATGCT                                                                                         <  2:301893/141‑1

                                                GCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAAGACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATG                                                                                      >  1:438419/1‑143

                                                  TGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGCACAGGAAAGAATATGCTATGAA                                                                                    >  2:696461/1‑143

                                                     ACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCC                                                                                 <  1:322297/143‑1

                                                         GAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTAT                                                                             >  1:690572/1‑143

                                                          AGGGACAGCTGAGAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTCGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAGCCCTTATA                                                                            <  2:562365/143‑1

                                                             GACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTT                                                                         <  2:782542/143‑1

                                                                  CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTT                                                                    <  1:677336/143‑1

                                                                    GATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATATACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGG                                                                  <  1:693640/143‑1

                                                                     ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGT                                                                 <  1:81964/143‑1

                                                                       AGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCCCCCTGTAGTCCAATTCTCTCCAGTTTGAACAGGAACGAATATGCTATGAACACTTATATTTAACTAGGTGG                                                               >  1:94263/1‑143

                                                                       AGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATAGGCTATGAACCCTCATATTCATCTTGGTGG                                                               >  2:833427/1‑143

                                                                           ACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTGATATTTATCTCGGTGGTGCA                                                           >  2:720335/1‑143

                                                                                    ACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACGTGCA                                                  >  1:774587/1‑143

                                                                                       GGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAG                                               <  1:485265/143‑1

                                                                                          GCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTC                                            >  1:680023/1‑143

                                                                                               TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGG                                       >  1:310266/1‑143

                                                                                                CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGT                                      >  2:643888/1‑143

                                                                                                 AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCGGTTTGAGCAGGAAAGAATATGCTATGAACCCTTATAGTCATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTA                                     >  2:728865/1‑143

                                                                                                    AACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAA                                  <  1:239475/143‑1

                                                                                                         CATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTACAGAGGTCAGTGGTACAACCTTA                             >  2:131112/1‑143

                                                                                                              TACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAAGCTTAATGAA                        >  1:581874/1‑143

                                                                                                                 ACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTT                     <  1:405340/143‑1

                                                                                                                   TAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTACTGAAGTTTT                   >  2:221544/1‑143

                                                                                                                        catTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAA              <  1:121168/140‑1

                                                                                                                                    AGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGG  <  1:176676/143‑1

CGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258535‑258675

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGG  >  NC_000913/568268‑568401

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `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