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 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,304,813	(C)_7→8	coding (1005/1245 nt)	mtr ←	tryptophan:H(+) symporter Mtr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,304,806	1	.	C	100.0%	142.4 / NA	41	L338V (CTG→GTG)	mtr	tryptophan:H(+) symporter Mtr
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (26/15); total (26/15)

ACCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAA  >  NC_000913/3304669‑3304930

aCCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑cc                                                                                                                            <  1:773971/140‑1 (MQ=255)

aCCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑cc                                                                                                                            <  1:721760/140‑1 (MQ=255)

  cccAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑cccc                                                                                                                          <  1:605644/140‑1 (MQ=255)

     aGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑ccccccc                                                                                                                       <  1:39209/140‑1 (MQ=255)

       aCGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑ccccccccc                                                                                                                     >  2:115605/1‑138 (MQ=255)

          cgGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑ccccccccacaa                                                                                                                  <  2:867529/140‑6 (MQ=255)

            gAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACt                                                                                                                 >  1:280982/1‑140 (MQ=255)

                     gCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCa                                                                                                        <  1:703156/140‑1 (MQ=255)

                      cTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCaa                                                                                                       <  2:280982/140‑1 (MQ=255)

                         ccAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAgg                                                                                                    >  2:502323/1‑140 (MQ=255)

                                         aTGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTAGAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGtttt                                                                                    >  2:774921/1‑140 (MQ=255)

                                             ccGGGCTAACCACGCCGGAACAACCGCCGCCCACATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg                                                                                <  2:589385/139‑1 (MQ=255)

                                             aCGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg                                                                                <  1:794139/140‑1 (MQ=255)

                                                    aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCca                                                                         >  2:390065/1‑140 (MQ=255)

                                                    aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCca                                                                         >  1:550960/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  2:230938/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  2:13458/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  <  2:121107/140‑1 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  2:551525/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  1:797679/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  1:121107/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  1:794595/1‑140 (MQ=255)

                                                           ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGa                                                                  >  1:526208/1‑140 (MQ=255)

                                                                        cgccCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCa                                                     <  2:550960/140‑1 (MQ=255)

                                                                             aGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAg                                                <  1:502323/140‑1 (MQ=255)

                                                                                    aGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCTGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGcc                                         >  1:573610/1‑140 (MQ=255)

                                                                                     gCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCTGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCa                                        <  2:573610/140‑1 (MQ=255)

                                                                                     gCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCa                                        <  1:690850/140‑1 (MQ=255)

                                                                                     gCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCa                                        <  1:773455/140‑1 (MQ=255)

                                                                                      ccGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAg                                       >  1:513546/1‑140 (MQ=255)

                                                                                         cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGaca                                    >  1:182233/1‑138 (MQ=255)

                                                                                         cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATa                                    >  1:262759/1‑140 (MQ=255)

                                                                                         cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATa                                    >  2:542925/1‑140 (MQ=255)

                                                                                                aGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTcaaa                              <  1:447211/140‑1 (MQ=255)

                                                                                                     aaCCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAAcc                        <  1:551525/140‑1 (MQ=255)

                                                                                                            ggCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGGTTTCAAGCGGCCCCCAACCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGtt                 >  2:778471/1‑140 (MQ=255)

                                                                                                                tACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGc             >  1:356608/1‑140 (MQ=255)

                                                                                                                tACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGc             >  1:837717/1‑140 (MQ=255)

                                                                                                                tACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGc             >  2:66253/1‑140 (MQ=255)

                                                                                                                  cAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCg           <  1:542925/140‑1 (MQ=255)

                                                                                                                  cAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCg           >  2:866051/1‑140 (MQ=255)

                                                                                                                     gAATCCGTTCGGGAACAACAGCCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAg         >  1:22610/1‑140 (MQ=255)

                                                                                                                        tCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaac     >  2:138008/1‑140 (MQ=255)

                                                                                                                        tCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaac     >  1:804424/1‑140 (MQ=255)

                                                                                                                           gTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacgaa  <  2:629292/140‑1 (MQ=255)

                                                                                                                               gggAACAACAGC‑CCCCCCCACAACTGGTGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCg           <  2:155746/127‑1 (MQ=255)

                                                                                                                               gggAACAACAGC‑CCCCCCCACAACTGGTGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCg           >  1:155746/1‑127 (MQ=255)

ACCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAA  >  NC_000913/3304669‑3304930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A