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
A17 F1 I1 R1	15	26.4	1686296	95.9%	1617157	76.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	REL606	4,524,522	IS186 (+) +6 bp	coding (494‑499/549 nt)	fimA →	major type 1 subunit fimbrin (pilin)

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	REL606	2772854 =	NA (NA)	25 (0.990)	21/144	0.3	100%	noncoding (1/1343 nt)	IS186	repeat region
*	?	REL606	= 4524527	0 (0.000)	25 (0.990)	21/144	0.3	100%	coding (499/549 nt)	fimA	major type 1 subunit fimbrin (pilin)
*	?	REL606	= 2774196	NA (NA)	25 (0.990)	23/144	0.2	100%	noncoding (1343/1343 nt)	IS186	repeat region
*	?	REL606	4524522 =	0 (0.000)	25 (0.990)	23/144	0.2	100%	coding (494/549 nt)	fimA	major type 1 subunit fimbrin (pilin)

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/2772931‑2772854

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTT  <  REL606/4524527‑4524460

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATG                                                                        >  1:460371/1‑76

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATG                                                                        <  1:517696/76‑1

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATG                                                                        <  2:605231/76‑1

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATAGCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATG                                                                        <  1:708869/76‑1

GTTATCGNGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATG                                                                        >  2:682879/1‑76

 TTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGG                                                                       >  1:241135/1‑76

 TTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGG                                                                       <  2:76938/76‑1

     CGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTG                                                                   <  2:279957/76‑1

            GTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCC                                                            >  1:262398/1‑76

              AATTCATCGGCACGTTAAATTATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGG                                                          >  2:516747/1‑76

              AATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGG                                                          >  2:247828/1‑76

                 TCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTG                                                       <  1:379718/76‑1

                  CATCGGCGCGTTAGATCATANCAGGCGTAATACCTCNACCCTTAAGTTAGCGTTTATGGGTTGCGGCCCCGGTTGC                                                      <  2:833321/76‑1

                          CGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAAC                                              >  1:623590/1‑76

                            TTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGC                                            >  2:447562/1‑76

                              AAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGC                                          >  1:537776/1‑76

                                 TCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTG                                       <  2:114346/76‑1

                                      TCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACG                                  <  1:800441/76‑1

                                              aagACCACGACCCTGAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCATGGAACGGAATGGTA                          <  2:70814/73‑1

                                               ATACCACAACCCTTNAGTTAGCGCTTATGGGTTGCGGCCCCGCTTGCAAAATAACGCGCCGGGCACGGAATGGTAT                         <  1:719889/76‑1

                                               ATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGTCCTCGGTTGCANAATAACGCGCCTGGAACGGAATGGTAT                         <  1:740658/76‑1

                                               ATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTAT                         <  2:97663/76‑1

                                                TACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATT                        >  1:184464/1‑76

                                                TACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATT                        <  1:463257/76‑1

                                                 ACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTG                       <  2:759517/76‑1

                                                  CCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGGATTGG                      >  2:648923/1‑76

                                                     CAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTC                   <  2:808222/76‑1

                                                       ACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCG                 >  2:580995/1‑76

                                                           TTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTAT             >  1:369936/1‑76

                                                             AAGTTAGCGCTTATGGGTTGCGGCCCCTGTTGCANAATATCGNGCNTGNAACGTCATGGTATTGGTTCCGTTATTC           >  1:734229/1‑76

                                                                    CGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTG    <  1:682879/76‑1

                                                                      CTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTT  <  2:425685/76‑1

GTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/2772931‑2772854

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTT  <  REL606/4524527‑4524460

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `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