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 F166 I0 R1	50	63.8	1389156	94.9%	1318309	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%	131.5 / ‑6.5	42	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (18/23); total (18/24)
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.

TTTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAG  >  CP000730/1105857‑1106127

tttGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACcata                                                                                                                                    >  1:479524/1‑141 (MQ=255)

  tGACCACACACAAATTGGTGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGt                                                                                                                                  <  2:430089/141‑1 (MQ=255)

   gACCACAGACCAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTACATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTa                                                                                                                                 <  1:469122/141‑1 (MQ=255)

   gACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTACATAATCGAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTa                                                                                                                                 >  2:75747/1‑141 (MQ=255)

     ccACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAAt                                                                                                                               >  2:211199/1‑141 (MQ=255)

                      gTGCAACTGGCCAACATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCGAATTGAAACGAATACCATAGTAATCGGAGAAGGTCCtggtg                                                                                                              >  2:417347/1‑141 (MQ=255)

                         cAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATACCGAATTGTGATTAATGGAGGGTGAGAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGAt                                                                                                           <  1:302587/141‑1 (MQ=255)

                           aCTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATAc                                                                                                         >  1:220816/1‑141 (MQ=255)

                                gaaaaaTGCAATTAATCAAATTAAACGTTTATCAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTCCCCAATTGAAACAGATACCATAGTACTCGGAGCAGGTCCTGGTGGATACGTTgc                                                                                                    <  2:110418/139‑1 (MQ=255)

                                        cAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTc                                                                                            >  1:688623/1‑141 (MQ=255)

                                        cAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCAGAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTc                                                                                            <  1:41848/141‑1 (MQ=255)

                                           tGAATCACATTAGACGTTTATTAAATAATCCAGGATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTg                                                                                         <  2:53811/141‑1 (MQ=255)

                                             aaTCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCa                                                                                       <  1:222399/141‑1 (MQ=255)

                                             aaTCACATTAAACGGTTATTAAATAACCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCa                                                                                       <  1:575600/141‑1 (MQ=255)

                                              aTCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAg                                                                                      >  1:212502/1‑141 (MQ=255)

                                                      aaaCGTTTATTAAATAATACAGAATTATTATTAATGGAGGGGTAAAACATGTTAATTGGAGATTTTCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCCATTa                                                                              <  1:473299/141‑1 (MQ=255)

                                                      aaaCGGTTATTAAACAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTa                                                                              <  2:19182/141‑1 (MQ=255)

                                                                taAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAg                                                                    >  1:517102/1‑141 (MQ=255)

                                                                   ataatCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTaa                                                                 <  1:211199/141‑1 (MQ=255)

                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGTACAAAAGGTAAGAAtg                                                            >  1:675959/1‑140 (MQ=255)

                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATc                                                            >  1:111383/1‑141 (MQ=255)

                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATc                                                            <  1:280418/141‑1 (MQ=255)

                                                                             attattattAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGTATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTga                                                       <  1:462907/141‑1 (MQ=255)

                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:388934/1‑141 (MQ=255)

                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:135674/1‑141 (MQ=255)

                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:206784/1‑141 (MQ=255)

                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:304084/1‑141 (MQ=255)

                                                                                   attaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGGCCGGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAgg                                                 >  1:317265/1‑141 (MQ=255)

                                                                                          gAGTGGTAAAACATGGTAGATGGAGATTTCACAAATGATACAGATACCATAGTAATTGGAGCAAGACCTGGTGGATACGGTGCAACAATTCGTGCAGCTCAATTAAGACAAAAAGTAACAATCGTTGAGAAAGGTAATCtt                                          <  2:256230/141‑1 (MQ=255)

                                                                                          gAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCtt                                          <  1:30036/141‑1 (MQ=255)

                                                                                             ggagaaaaCATGGTAGTTGGAGCGTTCCGAATTGAAACAGATACCAGATTAATCGTAGAAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGATCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggt                                       <  2:693011/137‑1 (MQ=255)

                                                                                               gtacaccATGGTAGTTGGACATTGCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  2:368459/135‑1 (MQ=255)

                                                                                               gTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  1:19406/141‑1 (MQ=255)

                                                                                               atAACACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGGCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  2:95088/140‑1 (MQ=255)

                                                                                                  aaaCCTGGTAGTTTGAGATTTCCCAATTTAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGgtgt                                  <  2:67272/141‑1 (MQ=255)

                                                                                                   aaCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTgttgtt                                 >  1:434123/1‑141 (MQ=255)

                                                                                                              tggttaTTTCCTAATTGTAACAGACACCATAGTAATGGTAGCGGGTCCTGATGAAAACGATGCAGCAATTCGTGGCGCTCGATTAGGCCAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGt                      <  2:425606/136‑1 (MQ=255)

                                                                                                                 agaTTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAgg                   >  2:343906/1‑141 (MQ=255)

                                                                                                                     ttCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGt               >  1:80291/1‑141 (MQ=255)

                                                                                                                      tcacAATTGAAACAGATACTCTATGAGGCGTAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTa              <  2:484950/138‑1 (MQ=255)

                                                                                                                              gAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATACCTTCa      >  2:588510/1‑141 (MQ=255)

                                                                                                                                  cAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCAAAAAAAAAAAAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAg  <  2:688623/141‑1 (MQ=255)

                                                                                                                                  cAGAGACCATAGTAATTGGAGCAGGTGCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAACGTAACGATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAg  <  2:212502/141‑1 (MQ=255)

TTTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAG  >  CP000730/1105857‑1106127

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