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 F3 I122 R1	193	20.9	1228102	94.7%	1163012	84.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,338,978	A→C	intergenic (‑417/+154)	dcuB ← / ← dcuR	anaerobic C4‑dicarboxylate transporter DcuB/two‑component system response regulator DcuR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,338,978	0	A	C	100.0%	24.5 / NA	8	intergenic (‑417/+154)	dcuB/dcuR	anaerobic C4‑dicarboxylate transporter DcuB/two‑component system response regulator DcuR
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (5/3); total (5/3)

CTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAACACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTT  >  NZ_CP009273/4338892‑4339050

cTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAccac                                                                       <  1:166769/90‑1 (MQ=255)

cTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAccac                                                                       <  2:351778/90‑1 (MQ=255)

   aTCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGt                                                                    <  1:549506/90‑1 (MQ=255)

     cTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTc                                                                  <  1:557021/90‑1 (MQ=255)

                                      gggTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATgg                                 >  2:111496/1‑90 (MQ=255)

                                       ggTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGa                                >  2:472365/1‑90 (MQ=255)

                                       ggTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGa                                >  2:79973/1‑90 (MQ=255)

                                                    ttaattaaCTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGa                                >  1:172299/1‑77 (MQ=255)

                                                    ttaattaaCTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGa                                <  2:172299/77‑1 (MQ=255)

                                                                     gCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGtt  >  1:473185/1‑90 (MQ=255)

CTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAACACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTT  >  NZ_CP009273/4338892‑4339050

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAACACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTTTTACTGATGAAGGATGTAACTTGTGCC  >  NZ_CP009273/4338892‑4339077

CTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTG                                                                                        <  SRR3721989.169813/100‑1 (MQ=60)

   ATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAG                                                                                     <  SRR3721989.561386/100‑1 (MQ=60)

     CTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAG                                                                                   <  SRR3721989.569104/100‑1 (MQ=60)

                                      ccttacgtcgtcggcagcgtcagatgtgtataagagacagAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATT                                                  <  SRR3721989.335474/60‑1 (MQ=60)

                                          GACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTActg                                              >  SRR3721989.175465/1‑97 (MQ=60)

                                                           ACTTTTGTTAGCGTTTTGAAATTAAAACCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTT                             >  SRR3721989.483137/1‑100 (MQ=60)

                                                                                      CCACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTTTTACTGATGAAGGATGTAACTTGTGCC  >  SRR3721989.74178/1‑100 (MQ=60)

CTGATCTACCCATTTGTGGGTAAAAATACACATAATGCGGGTGACATAATAGTTAATTAACTTTTGTTAGCGTTTTGAAATTAAAAACACCGTTCACCTGAAGAGATATTAATTTTTAGCGATGATGGAGGGATAATTATATTTGATCTGGCACAAGTTTTACTGATGAAGGATGTAACTTGTGCC  >  NZ_CP009273/4338892‑4339077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `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: `‑`