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 I1 R2	26	38.4	896262	90.9%	814702	136.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,105,994	T→C	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	93.5%	89.0 / ‑3.4	31	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (2/0); new base C (10/19); total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAGCA  >  CP000730/1105861‑1106129

aCCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTaa                                                                                                                                  <  1:178820/141‑1 (MQ=255)

 ccACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAAt                                                                                                                                 <  1:195679/141‑1 (MQ=255)

        cAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCa                                                                                                                          <  1:7286/141‑1 (MQ=255)

            ttGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTc                                                                                                                      <  2:105829/141‑1 (MQ=255)

                  gTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCtggtg                                                                                                                >  1:112236/1‑141 (MQ=255)

                              aaaaTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcag                                                                                                    <  1:405695/141‑1 (MQ=255)

                               aaaTGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTgcagc                                                                                                   <  2:66506/141‑1 (MQ=255)

                                   gCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAAtt                                                                                               <  2:238100/141‑1 (MQ=255)

                                   gCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAAtt                                                                                               <  2:238118/141‑1 (MQ=255)

                                      aTGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAATAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGt                                                                                            >  1:194702/1‑141 (MQ=255)

                                      aTGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGt                                                                                            >  2:334588/1‑141 (MQ=255)

                                         aaTCACATTAAACGTTTATTCAATTATCCAGAATTATTATTAATGGAGGAGTAAAAAATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCa                                                                                         <  1:221045/141‑1 (MQ=255)

                                                tagtgtttttATTAAATAATACAGAATTATTATTAATTTAGTTGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAAt                                                                                  <  1:422232/134‑1 (MQ=255)

                                                     cGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCGCAATCGAAACAGATACTAAAAGAATCGGAGCAGGTCATGGTGGATACGTGGCAGCAATTCGTGCAGCTCAATGAGGa                                                                             >  2:234033/1‑141 (MQ=255)

                                                     cGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGa                                                                             >  1:429807/1‑141 (MQ=255)

                                                        ttattaAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACaa                                                                          >  1:315702/1‑141 (MQ=255)

                                                             aaaTAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGt                                                                     >  2:216784/1‑141 (MQ=255)

                                                                gaatCCAGAATTATTATTAATGGAGGGGTAAAACGTGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAAc                                                                  <  1:166526/140‑1 (MQ=255)

                                                                    ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATc                                                              >  1:413263/1‑141 (MQ=255)

                                                                              tattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAg                                                    <  1:180384/141‑1 (MQ=255)

                                                                                 taATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTa                                                 <  1:140965/141‑1 (MQ=255)

                                                                                 taATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTa                                                 <  2:256674/141‑1 (MQ=255)

                                                                                           gTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                       <  1:200532/141‑1 (MQ=255)

                                                                                           gTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                       <  1:406217/141‑1 (MQ=255)

                                                                                            aaaaaCATGGTTGTTGGAGATTTCCAAAATGAAACAGATACCATAGTAATCGGAGAAGGAACTAGTGGATACGTTGCAGCAATTCGTGCAGAAAAAAAAAAAAAAAAAGTAACAATCGTTGAGAAAGGTAATCTTggtggt                                      <  2:404554/140‑1 (MQ=255)

                                                                                                      tAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTaa                            <  1:245258/141‑1 (MQ=255)

                                                                                                          tGGAGATTTCCCAAGTGAAACAGATACCATAGTAATCGGAGCAGGTCCGGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAACCTTGGTGGTGTGTGCTGAAACGt                        >  2:446544/1‑141 (MQ=255)

                                                                                                                              cAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAg    <  2:235674/141‑1 (MQ=255)

                                                                                                                               aGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAGc   >  1:143431/1‑141 (MQ=255)

                                                                                                                               aGATACCAAAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAAGCGTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAga   >  2:1033/1‑140 (MQ=255)

                                                                                                                                gATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAGCa  >  1:50526/1‑141 (MQ=255)

ACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAGCA  >  CP000730/1105861‑1106129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A