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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	607,884	G→A	100%	R209* (CGA→TGA)	dck ←	deoxynucleoside kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	607,884	0	G	A	100.0%	78.1 / NA	28	R209* (CGA→TGA)	dck	deoxynucleoside kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (12/16); total (12/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCC  >  CP000730/607752‑608018

gtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTCTGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCACGCAAttt                                                                                                                                >  2:100371/1‑141 (MQ=255)

          ttATTCGATAGTATTGAGAAAAAAATCGCTAATTTCTATGGAACAAACATGGAATATAAGCATATACGCTACGTCTTTAGTCTTGTATCGTGTATCTACATGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCAt                                                                                                                      <  2:262138/140‑1 (MQ=255)

          ttATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTGTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCAt                                                                                                                      <  1:288117/140‑1 (MQ=255)

                    gAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTaaa                                                                                                            >  2:431173/1‑141 (MQ=255)

                                     gATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTCTCTACTTGTCGATATGTTTGAATAATTCAAGCAATTATGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATg                                                                                           <  2:344570/141‑1 (MQ=255)

                                             ttATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCat                                                                                   <  1:301719/140‑1 (MQ=255)

                                                  gAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTct                                                                              >  2:151442/1‑140 (MQ=255)

                                                   aaTATACATTGAATATAAACATATACGCTATGTCGTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTGCTTATGGTTATCATATTGAt                                                                             >  1:180010/1‑141 (MQ=255)

                                                    atatACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCAtt                                                                            <  1:266207/141‑1 (MQ=255)

                                                        aCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTAGGGATATCATAttagttagta                                                                        >  1:76531/1‑133 (MQ=255)

                                                             gAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGAt                                                                   <  1:431173/141‑1 (MQ=255)

                                                               atatAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATAc                                                                 <  1:23901/141‑1 (MQ=255)

                                                                   aaaCATATACGCGATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGAAATTTTGTTTGTCATAGGATTTAAAGATTCGGGGTCCTTATGGATATAATATTCTTTAATATTGTTACGTAc                                                             >  1:155370/1‑141 (MQ=255)

                                                                      cATATACGCTATGTCTTTAGTCTTTTATCTTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAAc                                                          <  2:372281/141‑1 (MQ=255)

                                                                       atatACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTAAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATAAGTACAACt                                                         >  1:297345/1‑141 (MQ=255)

                                                                        tataCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTg                                                        >  1:312471/1‑141 (MQ=255)

                                                                             gCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACAt                                                   <  2:190012/141‑1 (MQ=255)

                                                                                 tGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACCACTGGACATGCAt                                               >  2:268857/1‑141 (MQ=255)

                                                                                 tGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAt                                               <  2:157832/141‑1 (MQ=255)

                                                                                     tttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTaaa                                           >  1:329967/1‑141 (MQ=255)

                                                                                      ttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                          >  2:447495/1‑141 (MQ=255)

                                                                                           tttttATCTTGTATCTACGTGTCGATATGTTTTAATTAGTCAAGCTATTTTGTTTATCATAGGATTTAAAGATGCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAGTAAAGCTAtt                                     <  2:263189/140‑1 (MQ=255)

                                                                                              ttATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAAt                                  >  1:453071/1‑141 (MQ=255)

                                                                                                            cTTGGCGATATGTTTGAATAATTCAATCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGc                    <  1:280292/141‑1 (MQ=255)

                                                                                                             atGTCGATATATTTGAATAATTCAAGCAATTTTGTTTAACATAGGAATTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATGAAAGCTATTAATCCAATCGCCATAGCg                   <  2:308345/140‑1 (MQ=255)

                                                                                                                tCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGttt                <  2:229700/141‑1 (MQ=255)

                                                                                                                             ataatTCAAGCAATTTCTTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTc   <  1:79433/141‑1 (MQ=255)

                                                                                                                              taatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTcc  <  1:100371/141‑1 (MQ=255)

GTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCC  >  CP000730/607752‑608018

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A