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
A1 F2 I227 R1	223	21.3	1167702	97.0%	1132670	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,494,539	T→C	F222S (TTC→TCC)	nanX →	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,494,539	0	T	C	100.0%	94.1 / NA	29	F222S (TTC→TCC)	nanX	MFS transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/15); total (14/15)

AGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG  >  NZ_CP009273/4494452‑4494625

aGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTccc                                                                                      >  2:25247/1‑90 (MQ=255)

aGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTccc                                                                                      <  2:216724/90‑1 (MQ=255)

aGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTccc                                                                                      <  1:80407/90‑1 (MQ=255)

   aGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCg                                                                                   <  2:256873/90‑1 (MQ=255)

                tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt                                                                      >  1:412957/1‑90 (MQ=255)

                tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt                                                                      >  1:85649/1‑90 (MQ=255)

                   atatAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTAtt                                                                   <  1:177387/90‑1 (MQ=255)

                        aGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTg                                                              >  2:439728/1‑90 (MQ=255)

                        aGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTg                                                              >  2:434687/1‑90 (MQ=255)

                        aGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTg                                                              <  1:495691/90‑1 (MQ=255)

                        aGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTg                                                              >  1:566550/1‑90 (MQ=255)

                             aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  2:541586/1‑90 (MQ=255)

                             aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  2:123045/1‑90 (MQ=255)

                             aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  2:375008/1‑90 (MQ=255)

                             aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         <  2:476880/90‑1 (MQ=255)

                             aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  1:131592/1‑90 (MQ=255)

                               aTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTg                                                       <  2:244051/90‑1 (MQ=255)

                                   aCATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCg                                                   >  2:40450/1‑90 (MQ=255)

                                    cATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGa                                                  <  2:428216/90‑1 (MQ=255)

                                         ttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAAc                                             <  1:442356/90‑1 (MQ=255)

                                                                 cTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCa                     <  1:329783/90‑1 (MQ=255)

                                                                     cAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATa                 >  2:549687/1‑90 (MQ=255)

                                                                        tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg              <  1:235409/90‑1 (MQ=255)

                                                                        tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg              <  1:10223/90‑1 (MQ=255)

                                                                          tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            <  1:541586/90‑1 (MQ=255)

                                                                          tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            <  2:566550/90‑1 (MQ=255)

                                                                          tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            >  1:178134/1‑90 (MQ=255)

                                                                           ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAg           >  2:565996/1‑90 (MQ=255)

                                                                             aTGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGtt         <  2:77231/90‑1 (MQ=255)

                                                                             aTGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGtt         <  1:581153/90‑1 (MQ=255)

                                                                               gATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTaa       <  1:123045/90‑1 (MQ=255)

                                                                                   gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACa   >  1:51771/1‑90 (MQ=255)

                                                                                    tttcCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAg  <  1:25247/90‑1 (MQ=255)

AGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG  >  NZ_CP009273/4494452‑4494625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CCAGAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGGTCATTTC  >  NZ_CP009273/4494442‑4494635

CCAGAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCC                                                                                                <  SRR3722111.210620/100‑1 (MQ=60)

          AGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTT                                                                                      <  SRR3722111.81388/100‑1 (MQ=60)

                GGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCT                                                                                >  SRR3722111.419027/1‑100 (MQ=60)

                GGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCT                                                                                >  SRR3722111.86703/1‑100 (MQ=60)

                        GATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTG                                                                        >  SRR3722111.575456/1‑100 (MQ=60)

                             ATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAC                                                                   <  SRR3722111.179612/100‑1 (MQ=60)

                             ATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAC                                                                   >  SRR3722111.133243/1‑100 (MQ=60)

                                  AGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCC                                                              <  SRR3722111.503316/100‑1 (MQ=60)

                                                   TTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTC                                             <  SRR3722111.449014/100‑1 (MQ=60)

                                                                          TCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGA                      >  SRR3722111.180366/1‑100 (MQ=60)

                                                                           CTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAG                     <  SRR3722111.334204/100‑1 (MQ=60)

                                                                                  TCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATAC              <  SRR3722111.238224/100‑1 (MQ=60)

                                                                                  TCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATAC              <  SRR3722111.10352/100‑1 (MQ=60)

                                                                                   agCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACC             <  SRR3722111.182169/98‑1 (MQ=60)

                                                                                   CTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA             >  SRR3722111.52394/1‑100 (MQ=60)

                                                                                    TCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG            <  SRR3722111.550099/100‑1 (MQ=60)

                                                                                     CTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGT           <  SRR3722111.433264/100‑1 (MQ=60)

                                                                                       ATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGG         <  SRR3722111.590265/100‑1 (MQ=60)

                                                                                         GATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGGTC       <  SRR3722111.124586/100‑1 (MQ=60)

                                                                                            CGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGGTCATT    >  SRR3722111.564331/1‑100 (MQ=60)

                                                                                              TTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGGTCATTTC  <  SRR3722111.25565/100‑1 (MQ=60)

CCAGAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGTGGTCATTTC  >  NZ_CP009273/4494442‑4494635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`