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
A7 F184 I0 R1	45	69.8	1527574	94.8%	1448140	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	355,466	G→A	100%	P412S (CCA→TCA)	brnQ1 ←	LIVCS family branched chain amino acid:cation symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	355,466	0	G	A	100.0%	155.9 / NA	50	P412S (CCA→TCA)	brnQ1	LIVCS family branched chain amino acid:cation symporter
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/23); total (27/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGA  >  CP000730/355331‑355599

gAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAAACGATAATAGCAAAGAGCATGAATGATAca                                                                                                                                   >  1:231137/1‑140 (MQ=255)

             aaaaGCCTAGTAACGATGGGCCAATCATAACTAGGCAGTGAGCATTTATTAAGTGGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAAt                                                                                                                      >  1:492420/1‑140 (MQ=255)

                  ccTAGTAACGATGGGTCAATCAATACTAGACAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCACCTATGAAAACGATAAGAGGAAAGAGCATGAATGATACAAGCCAAGCTAAATCGata                                                                                                                 >  2:376259/1‑140 (MQ=255)

                    tAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGAAATc                                                                                                               >  2:226848/1‑140 (MQ=255)

                        aaCGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGGATAAATACATCGATTATGAAACCGATAATACCAAAGAGCATGAATGATACAAGCTAAGCTAAATCGATATCTGCt                                                                                                           <  1:462599/140‑1 (MQ=255)

                           gATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTaaa                                                                                                        <  1:584994/140‑1 (MQ=255)

                             agggTCAATCATTACTAGGCAGTTAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAgg                                                                                                      <  2:104250/139‑1 (MQ=255)

                              gggTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGt                                                                                                     >  1:595667/1‑140 (MQ=255)

                               ggTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTa                                                                                                    >  1:590631/1‑140 (MQ=255)

                                 tCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAAc                                                                                                  <  1:163325/140‑1 (MQ=255)

                                        ttACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATaa                                                                                           <  1:676713/140‑1 (MQ=255)

                                          aCTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAAc                                                                                         >  2:484371/1‑140 (MQ=255)

                                          aCTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAAc                                                                                         >  1:752855/1‑140 (MQ=255)

                                              ggCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGAtt                                                                                     <  1:619500/140‑1 (MQ=255)

                                              ggCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCAAAAACGAtt                                                                                     >  2:255459/1‑140 (MQ=255)

                                              ggCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGACGTATAAATACATCGATTATGAAACCGATAATTGCAAGGAGAATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGAtt                                                                                     <  1:105547/140‑1 (MQ=255)

                                                   tGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGAAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCaaa                                                                                >  1:587435/1‑140 (MQ=255)

                                                     aGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAAt                                                                              <  2:527790/140‑1 (MQ=255)

                                                         tttATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAaca                                                                          <  2:757290/140‑1 (MQ=255)

                                                           tattaAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGAGTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACAcc                                                                        <  2:657917/140‑1 (MQ=255)

                                                            attaAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCg                                                                       >  2:683924/1‑140 (MQ=255)

                                                            attaAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAAAAACACCg                                                                       >  1:266975/1‑140 (MQ=255)

                                                            attaAGTTGTCGCTTGTTTCGGACGGCGTATAAATAAATCGATTATGAAACCGATAATAGCAGAGAGCATGAATGATAAAAGCCAAGCTAAATCGATTTCTGCTAAAGGTAACATCATAAAGGATTTCAAAATAAGACCg                                                                       >  2:37021/1‑140 (MQ=255)

                                                                aGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGta                                                                   >  2:412871/1‑140 (MQ=255)

                                                                  ttGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGtaat                                                                 >  1:695857/1‑140 (MQ=255)

                                                                   tGTTGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGtaata                                                                <  2:141638/140‑1 (MQ=255)

                                                                   tGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGtaata                                                                <  2:746979/140‑1 (MQ=255)

                                                                        cTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGCATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGATg                                                           >  2:509120/1‑140 (MQ=255)

                                                                               cGGATGGCGTATGAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATACACGATTTCAAAATAACACCGTGTAATAAATTGAAACTAt                                                    >  1:537261/1‑140 (MQ=255)

                                                                                    ggCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAATATAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTaat                                               >  1:104162/1‑138 (MQ=255)

                                                                                       gTAGAAATACATTGATTATGAAACCGAAAATAGCAAAGCGCATGAATGATACAACCCAAGCTAAAACGATATCTGCTAAAGTTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTAtt                                            <  2:26919/140‑1 (MQ=255)

                                                                                                   cGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGaa                                >  1:546884/1‑140 (MQ=255)

                                                                                                   cGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGaa                                <  1:671906/140‑1 (MQ=255)

                                                                                                       tATGAAACCGATAATAGCAAAGGGCATGAATGATACAAGCAAAGATAAATCGATATCTGCTAAAGGTGCTTCCATAAACAATCTCCAAATTACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAaataa                            <  1:750847/140‑1 (MQ=255)

                                                                                                       tATGAAACCGATAATAGCAAAGAGCATGAATTATACAAGGCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAaataa                            <  2:387314/140‑1 (MQ=255)

                                                                                                       tATGAAACCGAAAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAaataa                            <  1:126594/140‑1 (MQ=255)

                                                                                                          gAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAaataataa                         >  1:389704/1‑138 (MQ=255)

                                                                                                          gAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAATTAAAACTAATTAGTATTTGTAAAATTGAAATAATCa                         >  1:50960/1‑140 (MQ=255)

                                                                                                              ccGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAGGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGt                     >  1:443734/1‑140 (MQ=255)

                                                                                                               cGATAATAGCAAAGAGCATGAAGGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGta                    <  2:385315/140‑1 (MQ=255)

                                                                                                                 ataataGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGtaat                  >  1:69068/1‑140 (MQ=255)

                                                                                                                   aataGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGGGTACTAAGTTGAGACTATTTAGTATATGTAAAATTGAAAAAATAAATAtaaaaa                >  2:465343/1‑140 (MQ=255)

                                                                                                                     taGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACa              <  1:671523/140‑1 (MQ=255)

                                                                                                                     taGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACa              <  1:299740/140‑1 (MQ=255)

                                                                                                                       gCAAAGAGCATGAATGAGACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTTAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGt            <  2:492420/140‑1 (MQ=255)

                                                                                                                        cAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGtt           <  1:47697/140‑1 (MQ=255)

                                                                                                                            gagCATGAATGATACAAGCCAAGCTAAATCGTTATCTGTTAAAGGTAACATCATATACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGa       <  1:255459/140‑1 (MQ=255)

                                                                                                                                atgaatgaTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCg   >  2:105512/1‑140 (MQ=255)

                                                                                                                                atgaatgaTACAAGCCAACCTCGCTCTTTATGTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCg   >  1:755198/1‑140 (MQ=255)

                                                                                                                                 tGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGGGCCGa  >  2:4856/1‑140 (MQ=255)

                                                                                                                                 tGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGa  >  2:4937/1‑140 (MQ=255)

                                                                                                                                 tGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGa  >  1:469071/1‑140 (MQ=255)

GAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGA  >  CP000730/355331‑355599

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