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 I76 R1	7	11.0	663162	95.7%	634646	85.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,267,804	Δ1 bp	coding (408/465 nt)	soxR →	redox‑sensitive transcriptional activator SoxR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,267,804	0	C	.	100.0%	30.4 / NA	9	coding (408/465 nt)	soxR	redox‑sensitive transcriptional activator SoxR
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (3/6); total (3/6)

TAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTT  >  NZ_CP009273/4267722‑4267879

tAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCtt                                                                     <  1:167163/90‑1 (MQ=255)

       gcTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGagaa                                                              >  2:171418/1‑90 (MQ=255)

                          ggATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCt                                           <  1:274515/90‑1 (MQ=255)

                                     ttGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGAt                                >  2:87222/1‑90 (MQ=255)

                                                  tCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTagc                   <  1:87222/90‑3 (MQ=255)

                                                    gcgcAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAgc                 <  1:120205/90‑1 (MQ=255)

                                                       cAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGcc              <  1:283373/90‑1 (MQ=255)

                                                            aTTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAg         <  1:280156/90‑1 (MQ=255)

                                                                   gTTGCGTAACTCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCtt  >  1:130869/1‑90 (MQ=255)

TAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTT  >  NZ_CP009273/4267722‑4267879

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGTTTTCCGGTCTTTGTC  >  NZ_CP009273/4267717‑4267902

TACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAG                                                                                       <  SRR3722214.218720/100‑1 (MQ=60)

     TAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAA                                                                                  <  SRR3722214.169898/100‑1 (MQ=60)

                               GGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGA                                                        <  SRR3722214.279725/100‑1 (MQ=60)

                                                       TCGCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACT‑‑AGCGCCACAAGGG                              <  SRR3722214.88591/100‑1 (MQ=60)

                                                         GCGCAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGG                              <  SRR3722214.122093/100‑1 (MQ=60)

                                                            CAGTGATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGC                           <  SRR3722214.288761/100‑1 (MQ=60)

                                                              GTGATTGCCCGTTGCGTAACTCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTT                         >  SRR3722214.132902/1‑100 (MQ=60)

                                                                 ATTGCCCGTTGCGTAACCCGGG‑GACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAG                      <  SRR3722214.285472/100‑1 (MQ=60)

                                                                                      GGGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGTTTTCCGGTCTTTGTC  <  SRR3722214.109098/100‑1 (MQ=60)

TACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGTTTTCCGGTCTTTGTC  >  NZ_CP009273/4267717‑4267902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`