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
A3 F1 I2 R1	58	36.1	1832140	90.7%	1661750	105.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,846,715	T→C	Q233R (CAG→CGG)	hycD ←	hydrogenase 3, membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,846,715	0	T	C	100.0%	75.8 / NA	21	Q233R (CAG→CGG)	hycD	hydrogenase 3, membrane subunit
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/9); total (12/9)

TGCTGTTTTCGAACAGCGCGATAACCAGGACGCCGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCTGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGCCCATT  >  NC_000913/2846581‑2846846

tGCTGTTTTCGAACAGCGCGATAACCAGGACGCCGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCaa                                                                                                                                 <  2:761572/139‑1 (MQ=255)

                       aCCAGGACGCCGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGa                                                                                                          <  2:597853/139‑1 (MQ=255)

                          aGGACGCCGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATAc                                                                                                       <  2:287220/139‑1 (MQ=255)

                                 cGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCAttt                                                                                                >  1:752981/1‑139 (MQ=255)

                                                     gCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAgccgctgc                                                                            >  1:444121/1‑139 (MQ=255)

                                                          cACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGccgctgccgctg                                                                       <  2:752981/139‑1 (MQ=255)

                                                                                 cggcggTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTg                                                >  1:899676/1‑139 (MQ=255)

                                                                                      gTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCagaga                                                             <  1:463993/121‑1 (MQ=255)

                                                                                      gTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCagaga                                                             >  2:463993/1‑121 (MQ=255)

                                                                                                      gTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATAc                                                                                                       >  2:763674/1‑63 (MQ=255)

                                                                                                      gTCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATAc                                                                                                       <  1:763674/63‑1 (MQ=255)

                                                                                                       tCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAg                                                                                                                        <  1:723608/45‑1 (MQ=255)

                                                                                                       tCCCCACGGAATAAACACCCCGACGAACATCCGCAACACCACCAg                                                                                                                        >  2:723608/1‑45 (MQ=255)

                                                                                                                  tAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAGgccgctgccgc                                                                         <  1:245830/81‑1 (MQ=255)

                                                                                                                  tAAACACCCCGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAGgccgctgccgc                                                                         >  2:245830/1‑81 (MQ=255)

                                                                                                                          ccGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGc       >  2:151620/1‑139 (MQ=255)

                                                                                                                          ccGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGc       >  2:474407/1‑139 (MQ=255)

                                                                                                                          ccGACGAACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGc       >  2:382242/1‑139 (MQ=255)

                                                                                                                              cgaACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGCCCAt   >  1:58288/1‑139 (MQ=255)

                                                                                                                              cgaACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGCCCAt   >  1:341405/1‑139 (MQ=255)

                                                                                                                               gaACATCCGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGCCCAtt  <  1:756496/139‑1 (MQ=255)

TGCTGTTTTCGAACAGCGCGATAACCAGGACGCCGACCACCAGTTTTACGATGGCAATCACCAGCGCCAGCAGCAGTCCACCGGCGGTGAAGGTTTCCATTTGTCCCCACGGAATAAACACCCCGACGAACATCTGCAACACCACCAGCTGTTTCAGGCTGATACCCCATTTCATGACGCCAAAGCCGCTGCCGCTGTATTCAGAGAGCGGGCCTTCCTGCAGCTCCTGCTCGGCTTCCGCCAGGTCGAACGGCAGTTTGCCCATT  >  NC_000913/2846581‑2846846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A