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 F73 I1 R1	26	44.8	1518598	99.2%	1506449	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,594,875	G→T	G202G (GGC→GGA)	livM ←	branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,594,875	0	G	T	100.0%	167.1 / NA	50	G202G (GGC→GGA)	livM	branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (21/29); total (21/29)

TGAACGTGTCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCGCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCAAGCCGT  >  NC_000913/3594739‑3595002

tGAACGTGTCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCg                                                                                                                               <  1:718881/140‑1 (MQ=255)

   aCGTGTCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGaaa                                                                                                                            >  1:580561/1‑140 (MQ=255)

    cGTGTCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAAc                                                                                                                           <  1:581525/140‑1 (MQ=255)

     gtgtCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAAcc                                                                                                                          <  1:171312/140‑1 (MQ=255)

     gtgtCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAAcc                                                                                                                          <  1:363540/140‑1 (MQ=255)

          ccAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAggg                                                                                                                     <  1:305395/140‑1 (MQ=255)

          ccAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAggg                                                                                                                     <  1:596638/140‑1 (MQ=255)

             gccgccTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGCTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATGTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTaa                                                                                                                  >  2:308903/1‑140 (MQ=255)

                 ccTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGAt                                                                                                              >  2:60093/1‑140 (MQ=255)

                            ggTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGt                                                                                                   >  2:568234/1‑140 (MQ=255)

                               aCGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCAc                                                                                                >  1:78580/1‑140 (MQ=255)

                               aCGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCAc                                                                                                <  2:421979/140‑1 (MQ=255)

                                    tGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCgcgc                                                                                           <  1:322725/140‑1 (MQ=255)

                                      aaCTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑aa                                                                                        >  2:644683/1‑140 (MQ=255)

                                                cGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCAcc                                                                              >  1:637451/1‑140 (MQ=255)

                                                   agagTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGa                                                                           <  1:568234/140‑1 (MQ=255)

                                                       tgtCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAAc                                                                       >  1:126900/1‑140 (MQ=255)

                                                       tgtCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAAc                                                                       >  1:654724/1‑140 (MQ=255)

                                                         tCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCg                                                                     <  1:175634/140‑1 (MQ=255)

                                                         tCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCg                                                                     >  2:175634/1‑140 (MQ=255)

                                                          cGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGa                                                                    <  2:703068/140‑1 (MQ=255)

                                                            gTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGc                                                                  <  2:78580/140‑1 (MQ=255)

                                                               tCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCCGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAgg                                                               >  2:133175/1‑140 (MQ=255)

                                                                         actgaTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCg                                                                     <  1:67516/124‑1 (MQ=255)

                                                                         actgaTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCg                                                                     >  2:67516/1‑124 (MQ=255)

                                                                         actgaTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCccgccg                                                     >  2:672097/1‑140 (MQ=255)

                                                                            gaTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCccgccgccg                                                  <  1:672097/140‑1 (MQ=255)

                                                                             aTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCcgccgccgc                                                 >  2:332072/1‑140 (MQ=255)

                                                                             aTTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCcgccgccgc                                                 <  1:308903/140‑1 (MQ=255)

                                                                              ttCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCt                                                <  2:637451/140‑1 (MQ=255)

                                                                               tCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTg                                               >  1:686860/1‑140 (MQ=255)

                                                                                   ttCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCAt                                           >  2:499206/1‑140 (MQ=255)

                                                                                   ttCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCAt                                           >  1:88636/1‑140 (MQ=255)

                                                                                   ttCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCAt                                           <  2:686860/140‑1 (MQ=255)

                                                                                   ttCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCAt                                           >  1:438988/1‑140 (MQ=255)

                                                                                   ttCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGACACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCAt                                           >  1:541027/1‑140 (MQ=255)

                                                                                            ccgGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGc                                  <  2:704098/140‑1 (MQ=255)

                                                                                            ccgGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGc                                  <  2:326183/140‑1 (MQ=255)

                                                                                            ccgGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGc                                  <  2:48743/140‑1 (MQ=255)

                                                                                                  aTTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCgg                            <  2:580561/140‑1 (MQ=255)

                                                                                                  aTTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCgg                            <  1:78318/140‑1 (MQ=255)

                                                                                                  aTTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCgg                            <  1:332072/140‑1 (MQ=255)

                                                                                                          gtTATTGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGcaggcagg                    >  2:536381/1‑140 (MQ=255)

                                                                                                               tGAGCAGCAATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAg               <  1:650808/140‑1 (MQ=255)

                                                                                                                   cagcaATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGc           >  1:751483/1‑140 (MQ=255)

                                                                                                                    agcaATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGcc          <  2:438988/140‑1 (MQ=255)

                                                                                                                      caATATGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCa        <  1:536381/140‑1 (MQ=255)

                                                                                                                       aaTATGCGCAAAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGCAAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCa        <  2:650888/140‑1 (MQ=255)

                                                                                                                        atatGCGCACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCAAg      <  2:88636/140‑1 (MQ=255)

                                                                                                                            gcgcACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCAAGCCGt  <  1:60093/140‑1 (MQ=255)

                                                                                                                             cgcACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAg               <  1:175247/126‑1 (MQ=255)

                                                                                                                             cgcACAATTTCTCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAg               >  2:175247/1‑126 (MQ=255)

TGAACGTGTCCCAGCCGCCTTCACGAGCGGTACGGCTGAACTCGAGTCCGAAGAGTGTCGGTTTCGGGATCTGACTGATTCCGTTCGGGCCGCCGGTAATTTCGGTGTTATTGAGCAGCAATATGCGCACAATTTCGCCGAAACCGAGGGTAACGATCGCCAGATAGTCACCGCGC‑AAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATCGGCAGGCAGGTCCAGAAGCCCAAGCCGT  >  NC_000913/3594739‑3595002

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A