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
A21 F63 I0 R1	92	32.2	718920	92.2%	662844	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,105,994	T→C	100%	T12T (ACT→ACC)	pdhD →	dihydrolipoyl dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,105,994	0	T	C	100.0%	90.2 / ‑6.5	30	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (14/14); minor base A (1/0); total (15/15)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTT  >  CP000730/1105867‑1106121

gACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAg                                                                                                                    <  1:132302/141‑1 (MQ=255)

  cAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCa                                                                                                                  <  1:98167/141‑1 (MQ=255)

    aaTTGGTGGTGCAACTGGCCAAAATACAATGAATCACACTAAATGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATCTCCCAATCGAAACAGATACCATCGTAATCGGAGCAgg                                                                                                                <  2:267543/141‑1 (MQ=255)

      ttGATGGTGCAACTTGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTc                                                                                                              <  2:101433/141‑1 (MQ=255)

       ttaTGTTGCAACTGGCCAAAATGGAATGAATCACAGTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAACCAGATACCATAGTAATCGGAGCAGGTcc                                                                                                             <  2:211871/139‑1 (MQ=255)

                     gCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTg                                                                                               <  2:271774/141‑1 (MQ=255)

                        aaaaTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGAAAGAGAAGAACTTGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcag                                                                                            <  1:260767/141‑1 (MQ=255)

                         aaaTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcagc                                                                                           >  1:48317/1‑141 (MQ=255)

                                aTGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTCGCAGCAATTCGt                                                                                    >  2:105366/1‑141 (MQ=255)

                                 tGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCGTGGTGGATACGTTGCAGCAATTCGTg                                                                                   <  2:222646/141‑1 (MQ=255)

                                          ttAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAAt                                                                          <  1:79939/141‑1 (MQ=255)

                                             aaCGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATAAGTTGAAGCAATTCGTTCAGcgccgttag                                                                       >  1:356096/1‑133 (MQ=255)

                                                         ataatCCAGAATTATTATTAAGGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGATCAATTAGGAAAAAAAGTaa                                                           >  1:158731/1‑141 (MQ=255)

                                                                      attattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGaa                                              >  2:326198/1‑141 (MQ=255)

                                                                      attattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACAATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCGGCTCAATTAGGACAAAAAGTAACAATCGTTGAGaa                                              >  2:347/1‑141 (MQ=255)

                                                                         attaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGGGCAGGTCCTGGTGGATACATTGCAGAAATTCGTGCAGCTCAATAAGGACAAAAAGTAACAATCGTTCAGCAAgg                                           >  2:356950/1‑141 (MQ=255)

                                                                          ttaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAACCAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGCGAAAGGt                                          >  2:48114/1‑141 (MQ=255)

                                                                               ggAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCt                                     >  1:300348/1‑141 (MQ=255)

                                                                               ggAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCt                                     >  1:300309/1‑141 (MQ=255)

                                                                                   gggTAAAACATTGTAATTGGCGGTTTCCCAAATGAAACCTATACGATAGTAATCGGGGCAGGTCGTGGTGAATACGTTCCAGCAAGTCGCGCAGCTCAATGATGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggt                                 <  2:154039/141‑1 (MQ=255)

                                                                                      tAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACGATCGTTGAGAAAGGTAATCTTggtggt                              >  2:104641/1‑141 (MQ=255)

                                                                                        aaaCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGGGgtgt                            >  1:166784/1‑141 (MQ=255)

                                                                                        aaaCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAAGCTTGgtggtgg                            >  2:242045/1‑140 (MQ=255)

                                                                                           cATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTg                         <  1:287649/141‑1 (MQ=255)

                                                                                           cATGCTAGTTGGTGCTTGCCTGACTGTAACAGATATCATAGTAAGCGGTGCCGGAACTGGTGGATACGTTGCAGCAATCCGTGCAGCTCCATTAGGCCAAATAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTg                         <  2:12434/141‑1 (MQ=255)

                                                                                            aTGGTAGTTTTAAGTTTCCAAAATGGAACAGATACCTCTGTTATCGGAATAATTCCTGTATTATACGATGCAGCAATTCGCGCAGCTCTATTAGGACAAAAAGTACCTATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGc                        <  2:267883/141‑1 (MQ=255)

                                                                                            aTGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGc                        >  2:253865/1‑141 (MQ=255)

                                                                                                  attGGAGATTTTACTATTCAAACAGATACCAAAGAAATCGGAGCAGGTCCTGGTGGATAAGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAAc                  <  2:117430/140‑1 (MQ=255)

                                                                                                                 aTTGAAACAGATACCATAGTAATCGTAGCATGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCt   <  1:96397/141‑1 (MQ=255)

                                                                                                                  ttGAAACAGATACCATAGTACTCGGAACAGATCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTATTCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCtt  >  1:263854/1‑141 (MQ=255)

GACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTT  >  CP000730/1105867‑1106121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A