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 I211 R1	223	18.0	1007644	96.3%	970361	85.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,848,051	T→G	F257C (TTT→TGT)	emrD →	multidrug efflux MFS transporter EmrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,848,051	0	T	G	100.0%	60.8 / NA	19	F257C (TTT→TGT)	emrD	multidrug efflux MFS transporter EmrD
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (13/6); total (13/6)

GCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGC  >  NZ_CP009273/3847967‑3848136

gCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTg                                                                                  >  1:266875/1‑90 (MQ=255)

          gCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGtt                                                                        >  2:210636/1‑90 (MQ=255)

                 ggCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGa                                                                 <  1:150814/90‑1 (MQ=255)

                             gggCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATaaa                                                     <  2:433884/90‑1 (MQ=255)

                              ggCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAAc                                                    <  2:266875/90‑1 (MQ=255)

                                 tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                 >  1:48765/1‑90 (MQ=255)

                                 tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                 >  2:142117/1‑90 (MQ=255)

                                 tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                 >  2:162707/1‑90 (MQ=255)

                                 tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt                                                 >  2:169405/1‑90 (MQ=255)

                                     cAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTtctc                                             <  1:346958/90‑1 (MQ=255)

                                            aCGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTa                                      >  2:126333/1‑90 (MQ=255)

                                              ggTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAt                                    >  2:469080/1‑90 (MQ=255)

                                              ggTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAt                                    >  1:449613/1‑90 (MQ=255)

                                                 cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg                                 >  2:100032/1‑90 (MQ=255)

                                                 cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg                                 >  2:371388/1‑90 (MQ=255)

                                                             tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCAt                                                                            >  2:225549/1‑35 (MQ=255)

                                                             tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCAt                                                                            <  1:225549/35‑1 (MQ=37)

                                                              aTTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATc                    <  1:169405/90‑1 (MQ=255)

                                                                                gCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCtggctggc  >  2:195099/1‑90 (MQ=255)

GCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGC  >  NZ_CP009273/3847967‑3848136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `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

TTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG  >  NZ_CP009273/3847957‑3848148

TTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTG                                                                                              >  SRR3722094.270853/1‑100 (MQ=60)

                acactaagatggtcgtcggcagcgtcagatgtgtataagagacagGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGG                                                                              <  SRR3722094.228593/55‑1 (MQ=60)

                           GGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATA                                                                   <  SRR3722094.152923/100‑1 (MQ=60)

                                 GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT                                                             >  SRR3722094.49451/1‑100 (MQ=60)

                                              GCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAT                                                >  SRR3722094.457523/1‑100 (MQ=60)

                                               CAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATG                                               <  SRR3722094.352711/100‑1 (MQ=60)

                                                                        ATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGC                      <  SRR3722094.171767/100‑1 (MQ=60)

                                                                                            GTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCCGGCTGGCTTGCTGATGTGG  >  SRR3722094.48922/1‑100 (MQ=60)

TTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG  >  NZ_CP009273/3847957‑3848148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`