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
A19 F57 I0 R1	85	36.1	800162	93.0%	744150	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%	78.2 / ‑6.5	26	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (11/13); minor base A (1/0); total (12/14)
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.

TGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTT  >  CP000730/1105859‑1106121

tGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAAGCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAga                                                                                                                            >  1:376216/1‑140 (MQ=255)

 gACCACAGACAAATTGCTGGTGCAACTGGCCAAAACGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTa                                                                                                                           <  1:117187/141‑1 (MQ=255)

      caGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCgg                                                                                                                      >  1:13028/1‑141 (MQ=255)

      aaGACAAATTGATGGTGCAACTGGCCAAAATTCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCgg                                                                                                                      <  2:261139/140‑1 (MQ=255)

          cAAATGGATGGGGCACCTGGACAAAATGCAATGAATCACATTAAACGTTTATAAAATAATCCAGAATTCTTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCAGAGTAATAGGGGCa                                                                                                                  >  2:11617/1‑141 (MQ=255)

                              ccAAAATGCAATGAATCACATTAAAAGTTTATTAAATAATCCAGAATTATTATTAATGCAGGGGTAAAACATGGTAGTTGGGGATTTCCCAATTGAAACAGA‑TACCATAGTAATCTGAGCAAGTCCTGGGGgttgcgttgc                                                                                              >  2:58169/1‑141 (MQ=255)

                                   aTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGTAGATTTCCTTAGGGAGACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCaa                                                                                         <  1:93517/141‑1 (MQ=255)

                                      cAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTc                                                                                      <  1:396324/141‑1 (MQ=255)

                                            aTCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAg                                                                                <  2:281924/141‑1 (MQ=255)

                                              cacaATAACCATTTATTAAATAATCAAGACTTATTATTAATGGACGGGTAAAATATGGTCGATGGAGATTTCACAATTGAAACAGA‑GACAGTAGTAATCGGGCCAGGTCCTGGTGGATACGTTGCAGGAATTCGTGAAGca                                                                              >  2:102192/1‑140 (MQ=255)

                                                        gTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGAc                                                                    <  1:113837/141‑1 (MQ=255)

                                                            attaAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCATTTCGTGCAGCGCAATTAGGACaaaa                                                                <  1:218474/141‑1 (MQ=255)

                                                             ttaAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TCCCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACaaaaa                                                               >  1:176032/1‑141 (MQ=255)

                                                                  taatCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAAc                                                          <  1:336695/141‑1 (MQ=255)

                                                                  aaatCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAAc                                                          <  2:298344/140‑1 (MQ=255)

                                                                                tattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAg                                            >  1:7812/1‑141 (MQ=255)

                                                                                            ggTAAAAACTGGTATTTTGAGAGTGCCAAATTGAACCAGAGTAC‑ATAGTAATCGGATTAGGTGCTGGTGGATACGCTGCAGCAACTCGTGCAGGGCAATTAGTACAACAATTAACAATCGTTGAGAAAGGTAATCTtggtg                                <  2:170318/141‑1 (MQ=255)

                                                                                              tAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtggg                              >  1:360744/1‑140 (MQ=255)

                                                                                              tAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTggtggt                              >  1:98679/1‑141 (MQ=255)

                                                                                              tAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGAGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAAAAATCGTTGAGAAAGGTAATCTTggtggt                              >  1:174238/1‑141 (MQ=255)

                                                                                               aaaaCATGGTAGGTGGAGATTTCTCAAGTGAGATAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAAGTCGTGCAACTCAATTAGGACAAAAAGTAACAATCGTGGAGAAAGGTACTCTTGgcggtg                             >  2:264062/1‑141 (MQ=255)

                                                                                                      gatacttGGATATTTAACAATTGAAACAGA‑TAACATAGTAATCGGAGCAGGTCCTGGTGGATAAGTTGCAGCAATTAGTGCAGCACAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCtt                      <  2:288861/136‑1 (MQ=255)

                                                                                                               agaTTTCCCAGTTGAAACAGA‑TGCCATAGAAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTATATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAgg             <  2:13028/141‑1 (MQ=255)

                                                                                                                 aTTTCCCAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGAt           >  1:61856/1‑141 (MQ=255)

                                                                                                                     cccAATTGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTAt       <  2:323396/141‑1 (MQ=255)

                                                                                                                          ttGAAACAGA‑TACCATAGTAATCGGAGCAGGTCCTGGTGGGTACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCtt  <  1:226537/141‑1 (MQ=255)

TGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGA‑TACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTT  >  CP000730/1105859‑1106121

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