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 I220 R1	9	22.2	1497724	96.2%	1440810	85.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	481,275	C→A	A20D (GCT→GAT)	acrR →	multidrug efflux transporter transcriptional repressor AcrR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	481,275	0	C	A	100.0%	35.2 / NA	11	A20D (GCT→GAT)	acrR	multidrug efflux transporter transcriptional repressor AcrR
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (6/5); total (6/5)

TAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGC  >  NZ_CP009273/481193‑481351

tAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGt                                                                       <  1:575259/90‑1 (MQ=255)

 aaCGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTc                                                                      >  1:106932/1‑90 (MQ=255)

       tGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTtct                                                                >  2:476379/1‑90 (MQ=255)

                  gAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAgggg                                                     >  2:355927/1‑90 (MQ=255)

                    aCATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGt                                                   >  2:252775/1‑90 (MQ=255)

                     cATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTa                                                  <  1:293890/90‑1 (MQ=255)

                     cATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTa                                                  <  2:621218/90‑1 (MQ=255)

                                           aagaagCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCgaga                            <  2:188123/90‑1 (MQ=255)

                                                  gcAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCaaa                     >  1:163301/1‑90 (MQ=255)

                                                             gcCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCg          >  1:206459/1‑90 (MQ=255)

                                                                     aTCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTAcgcgc  <  2:206459/90‑1 (MQ=255)

TAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGC  >  NZ_CP009273/481193‑481351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCG  >  NZ_CP009273/481178‑481343

gtataagagacagTCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGACAACACATCCTCGATGTGGATC                                                                    <  SRR3722103.576882/87‑1 (MQ=60)

AAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATC                                                                    <  SRR3722103.572334/100‑1 (MQ=60)

      ATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTC                                                              >  SRR3722103.108488/1‑100 (MQ=60)

               TAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCAC                                                     <  SRR3722103.585085/100‑1 (MQ=60)

                             tacacattgacattcgtcggcagcgtcagatgtgtataagagacaGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCA                                       <  SRR3722103.195694/55‑1 (MQ=60)

                                    CATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCT                                <  SRR3722103.298060/100‑1 (MQ=60)

                                                       AACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAA             >  SRR3722103.165721/1‑100 (MQ=60)

                                                                  CAAGAAACGCGCCAACACATCCTCGATGTGGATCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCG  >  SRR3722103.209470/1‑100 (MQ=60)

AAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCG  >  NZ_CP009273/481178‑481343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`