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 F117 I0 R1	36	24.6	540534	94.7%	511885	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%	82.8 / NA	27	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/15); total (12/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATT  >  CP000730/1105858‑1106117

ttGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAg                                                                                                                         >  2:137849/1‑141 (MQ=255)

    ccACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAAt                                                                                                                     >  1:80838/1‑141 (MQ=255)

       aaGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCgg                                                                                                                  <  2:252034/140‑1 (MQ=255)

         gACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAg                                                                                                                >  2:62085/1‑141 (MQ=255)

         gACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAg                                                                                                                >  2:206455/1‑141 (MQ=255)

                     gTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCtggtg                                                                                                    <  2:42941/141‑1 (MQ=255)

                      tGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCtggtgg                                                                                                   <  2:36479/141‑1 (MQ=255)

                      tGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCtggtgg                                                                                                   <  2:182736/141‑1 (MQ=255)

                               ccAAAATGCAATGAATCACAGTAAACGTTTATTGAATACTCCAGAATTATTATGACTGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGATACAGATACCATAGTAATCGGAGCTGGTCCTGGTGGATACGTTgc                                                                                          <  2:148612/141‑1 (MQ=255)

                                 aaaaTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcag                                                                                        >  1:106762/1‑141 (MQ=255)

                                  aaaTGCAATGAATCACATTAAACCTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTCCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcagc                                                                                       <  1:147386/141‑1 (MQ=255)

                                                    tAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAAtt                                                                     >  2:81841/1‑141 (MQ=255)

                                                      aaCGTTTATTAAATAATCCAGAATCATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAg                                                                   <  1:101907/141‑1 (MQ=255)

                                                      aaCGGTTATGAAATAAGCCAGAAGTATTATTGATGGGGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCAGAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAg                                                                   <  2:81639/141‑1 (MQ=255)

                                                       aCGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGGTACGTTGCAGCACTTCGGGCAGCGCGATTAgg                                                                  >  1:110603/1‑141 (MQ=255)

                                                                aaaTAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGt                                                         >  2:236378/1‑141 (MQ=255)

                                                                 aacattCCAGAATTCTTATTAATGGGTGGGTAAAACAGGGTAGTTGGAGATTTGCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGTAGCTCAATTAGGACAAAAAGTa                                                        <  2:543/136‑1 (MQ=255)

                                                                       ccAGCACTATTATCAATGGAGCGCTAAACCAGGGTAGTTGGAGATTCCCCAATCGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGGTGCAGCAATTCGTGCAGCTCAATTAGTACAAAAAGTAACACTc                                                  <  2:46007/141‑1 (MQ=255)

                                                                                  attaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAgg                                       >  1:110568/1‑141 (MQ=255)

                                                                                           ggggTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtgg                              <  2:80838/141‑1 (MQ=255)

                                                                                                          aGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTaaa               <  1:8514/141‑1 (MQ=255)

                                                                                                                agaTTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAgg         >  2:3751/1‑141 (MQ=255)

                                                                                                                agaTTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGCAATCTTGGTGGTGTTTGCTTAAACGTAgg         >  1:38543/1‑141 (MQ=255)

                                                                                                                     tCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTa    >  1:43836/1‑141 (MQ=255)

                                                                                                                       ccAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGGGTTCCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTAtt  <  1:62085/141‑1 (MQ=255)

                                                                                                                       ccAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTAtt  <  1:206455/141‑1 (MQ=255)

                                                                                                                       ccAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTAtt  <  1:236378/141‑1 (MQ=255)

TTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATT  >  CP000730/1105858‑1106117

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