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 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	441,393	A→C	F244V (TTC→GTC)	yajR ←	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	441,393	0	A	C	100.0%	107.4 / NA	31	F244V (TTC→GTC)	yajR	MFS transporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (16/15); total (16/15)

ACGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCAT  >  NZ_CP009273/441257‑441525

aCGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAccc                                                                                                                                    <  1:338182/139‑1 (MQ=255)

            aCGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCa                                                                                                                        <  2:86165/139‑1 (MQ=255)

                      cAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCggg                                                                                                              <  1:347856/139‑1 (MQ=255)

                               gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGcaa                                                                                                      >  1:563195/1‑138 (MQ=255)

                               gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGcaa                                                                                                      >  1:321622/1‑138 (MQ=255)

                                     ttttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCa                                                                                                                        >  1:171738/1‑114 (MQ=255)

                                     ttttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCa                                                                                                                        <  2:171738/114‑1 (MQ=255)

                                          cgcTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACa                                                                                          >  1:218976/1‑139 (MQ=255)

                                            cTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATc                                                                                        <  2:153981/139‑1 (MQ=255)

                                                 cTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCaa                                                                                   <  1:311268/139‑1 (MQ=255)

                                                    cAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCaaaa                                                                                 >  1:510247/1‑138 (MQ=255)

                                                       cGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATg                                                                             >  2:55917/1‑139 (MQ=255)

                                                       cGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATg                                                                             <  1:349026/139‑1 (MQ=255)

                                                            aTAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGa                                                                         >  1:187017/1‑138 (MQ=255)

                                                            aTAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGa                                                                         <  2:187017/138‑1 (MQ=255)

                                                                 gAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACAt                                                                    >  1:155427/1‑138 (MQ=255)

                                                                                      ggCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTcag                                               >  2:398115/1‑138 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATg                                                                             >  1:547270/1‑104 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATg                                                                             <  2:547270/104‑1 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGcc                                          >  1:564429/1‑139 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGcc                                          >  1:51983/1‑139 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGcc                                          >  2:556944/1‑139 (MQ=255)

                                                                                          aTTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGcc                                          >  2:319667/1‑139 (MQ=255)

                                                                                                   gTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTcc                                  <  2:321622/138‑1 (MQ=255)

                                                                                                      gCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCa                              <  2:218976/139‑1 (MQ=255)

                                                                                                      gCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCa                              <  2:51983/139‑1 (MQ=255)

                                                                                                                     cAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGaaa                <  1:162337/138‑1 (MQ=255)

                                                                                                                     cAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGaaa                <  1:398115/138‑1 (MQ=255)

                                                                                                                     cAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAAc               <  2:155427/139‑1 (MQ=255)

                                                                                                                             aGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCttt        >  1:255492/1‑138 (MQ=255)

                                                                                                                              gccgccGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCa      <  1:213939/139‑1 (MQ=255)

                                                                                                                                  ccgGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCAt  >  2:368008/1‑139 (MQ=255)

ACGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCAT  >  NZ_CP009273/441257‑441525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ACCACGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCATTCCGGACTC  >  NZ_CP009273/441254‑441534

cagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAG                                                                                                                                    <  SRR3722139.397950/89‑1 (MQ=60)

  CACGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCC                                                                                                                                  <  SRR3722139.342302/151‑1 (MQ=60)

                       GACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAAC                                                                                                              >  SRR3722139.569652/1‑150 (MQ=60)

                       GACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAAC                                                                                                              >  SRR3722139.325588/1‑150 (MQ=60)

                        ACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAA                                                                                                            <  SRR3722139.352069/151‑1 (MQ=60)

                             GACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCctgtctcttatacac                                                                                                       >  SRR3722139.173884/1‑136 (MQ=60)

                                  GCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACAT                                                                                                  >  SRR3722139.221654/1‑151 (MQ=60)

                                            GCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAAT                                                                                         >  SRR3722139.516124/1‑150 (MQ=60)

                                                   ACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGAC                                                                                 <  SRR3722139.315125/151‑1 (MQ=60)

                                                    CTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGAC                                                                                 >  SRR3722139.189348/1‑150 (MQ=60)

                                                         GCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAA                                                                           <  SRR3722139.353250/151‑1 (MQ=60)

                                                         GCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATA                                                                            >  SRR3722139.157327/1‑150 (MQ=60)

                                                                                  AGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAActgtctcttatacacatctccgagc                                                  >  SRR3722139.553561/1‑126 (MQ=60)

                                                                                  AGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCG                                                  >  SRR3722139.570906/1‑151 (MQ=60)

                                                                                  AGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCG                                                  >  SRR3722139.52577/1‑151 (MQ=60)

                                                                                                                     TTCCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTC                >  SRR3722139.258706/1‑150 (MQ=60)

                                                                                                                       CCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCAC              <  SRR3722139.402838/150‑1 (MQ=60)

                                                                                                                       CCAGTGTTCAGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCAC              <  SRR3722139.164335/150‑1 (MQ=60)

                                                                                                                                AGCCGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCATTCCGGAC    <  SRR3722139.216579/151‑1 (MQ=60)

                                                                                                                                   CGCCGGGACCCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCATTCCGGACTC  >  SRR3722139.406063/1‑150 (MQ=60)

ACCACGATCAACCCGACGCAGAAGACAAAGACTTGCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCATCAGCCAGTTGTCCGGGCAGGGCAACAAACGTCGACATCAGCAAAATATGCAGACACATAATGCCAAAGTTGAGTTTCAGCAGCCGCGGTTCCGCCAGCACTTTACTGAAACTGCCTTTCACCATTCCGGACTC  >  NZ_CP009273/441254‑441534

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`