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
A1 F169 I0 R1	132	34.5	794130	89.8%	713128	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,125,066	G→C	100%	E729Q (GAG→CAG)	pycA →	pyruvate carboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,125,066	0	G	C	100.0%	102.2 / NA	30	E729Q (GAG→CAG)	pycA	pyruvate carboxylase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (16/14); total (16/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTT  >  CP000730/1124936‑1125201

aTCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATc                                                                                                                               <  1:63643/141‑1 (MQ=255)

aTCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATAAGGCAGGCTTATTAAAACCTAAAGCCGCTTACGACATGATTGGTCAGTTAAAATc                                                                                                                               <  1:256697/141‑1 (MQ=255)

 tCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCa                                                                                                                              >  2:382944/1‑141 (MQ=255)

 tCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCa                                                                                                                              >  2:348981/1‑141 (MQ=255)

   aaaCATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAACCGCTTACGAATTGATTGGTCAGTTAAAAACAGc                                                                                                                            >  2:237448/1‑141 (MQ=255)

           ataCTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGAtt                                                                                                                    <  1:111313/141‑1 (MQ=255)

              cTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGTACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTAc                                                                                                                 >  2:65611/1‑141 (MQ=255)

                   gggTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATCGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAAtt                                                                                                            <  1:380331/139‑1 (MQ=255)

                                       tAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCTTGGTAc                                                                                        <  2:46670/141‑1 (MQ=255)

                                       tAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATAc                                                                                        <  1:357351/141‑1 (MQ=255)

                                          agggttataatctGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAg                                                                                     <  1:341383/129‑1 (MQ=255)

                                           gagTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGt                                                                                    >  1:143540/1‑141 (MQ=255)

                                                 gAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAAt                                                                              >  1:151445/1‑141 (MQ=255)

                                                 gAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAAt                                                                              >  1:200003/1‑141 (MQ=255)

                                                  aaCGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATg                                                                             >  1:279497/1‑141 (MQ=255)

                                                          ggTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGGAATGGTttatta                                                                     >  1:328090/1‑141 (MQ=255)

                                                           gataccATATTTTAGCGATTAAAGATATGGCACGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAACCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTaa                                                                    <  1:72305/137‑1 (MQ=255)

                                                                  tatTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATacaa                                                             <  1:391565/141‑1 (MQ=255)

                                                                  aatTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATacaa                                                             <  1:391501/140‑1 (MQ=255)

                                                                    ttttAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTAATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACAGTCATGATACAAGTGGGAATGGTTTATTAACATacaaaa                                                           >  1:116536/1‑140 (MQ=255)

                                                                      ttAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCATCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATacaaacaa                                                         <  1:269930/141‑1 (MQ=255)

                                                                                aagtacgggCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGCTTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATg                                               <  1:27917/134‑1 (MQ=255)

                                                                                aaGATATGGCAGGCTTGTTAATACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATCGAtt                                               >  1:203373/1‑140 (MQ=255)

                                                                                aaGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATg                                               >  1:237399/1‑141 (MQ=255)

                                                                                              ttattaAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATc                                 >  1:74196/1‑141 (MQ=255)

                                                                                                     aaCCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATa                          >  1:326328/1‑141 (MQ=255)

                                                                                                       ccTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAAAACGAAGAACATGCTGGTGTCGATATCATTGATAct                        <  1:191386/141‑1 (MQ=255)

                                                                                                            aGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGt                   <  2:388938/141‑1 (MQ=255)

                                                                                                                    aCGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGGGTCGATATCATTGATACTGCTGTTGCTTCaa           >  1:312496/1‑141 (MQ=255)

                                                                                                                             ttgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGTGTGGtt  >  2:27625/1‑141 (MQ=255)

ATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTT  >  CP000730/1124936‑1125201

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