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
A2 F28 I1 R1	129	74.0	2524844	99.2%	2504645	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,003,907	T→C	G12G (GGT→GGC)	fliD →	flagellar filament capping protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,003,907	0	T	C	100.0%	138.5 / NA	40	G12G (GGT→GGC)	fliD	flagellar filament capping protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (21/19); total (21/19)

ATTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGTCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCTGACGA  >  NC_000913/2003781‑2004037

aTTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGtt                                                                                                                       >  2:77570/1‑140 (MQ=255)

aTTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGtt                                                                                                                       <  2:108562/140‑1 (MQ=255)

aTTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGtt                                                                                                                       <  1:669947/140‑1 (MQ=255)

 ttAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTc                                                                                                                      <  1:908922/140‑1 (MQ=255)

 ttAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTc                                                                                                                      <  1:222648/140‑1 (MQ=255)

                      aaaCTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCAccgc                                                                                                 <  1:904538/140‑1 (MQ=255)

                        aCTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCAccgccg                                                                                               >  1:902435/1‑140 (MQ=255)

                             gcgcAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCaa                                                                                          >  2:171035/1‑140 (MQ=255)

                                             tAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAAccc                                                                          >  1:150248/1‑140 (MQ=255)

                                             tAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAAccc                                                                          >  1:322617/1‑140 (MQ=255)

                                             tAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAAccc                                                                          >  1:874057/1‑140 (MQ=255)

                                              aaCCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAAcccc                                                                         <  1:171035/140‑1 (MQ=255)

                                                       aTTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCaaa                                                                >  2:927002/1‑140 (MQ=255)

                                                           gTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCaa                                                                 <  2:432913/135‑1 (MQ=255)

                                                           gTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCaa                                                                 >  1:432913/1‑135 (MQ=255)

                                                           gTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAg                                                            <  1:503751/140‑1 (MQ=255)

                                                           gTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAg                                                            >  1:1027275/1‑140 (MQ=255)

                                                               tACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAAt                                                        <  1:473426/140‑1 (MQ=255)

                                                                aCGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAAtc                                                       >  2:486658/1‑140 (MQ=255)

                                                                      cGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGtt                                                 <  1:77570/140‑1 (MQ=255)

                                                                      cGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGtt                                                 <  2:1027275/140‑1 (MQ=255)

                                                                      cGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGtt                                                 <  2:322617/140‑1 (MQ=255)

                                                                        aaaGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTa                                               <  1:927002/140‑1 (MQ=255)

                                                                        aaaGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTa                                               <  2:874057/140‑1 (MQ=255)

                                                                             tAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCt                                          <  2:590282/140‑1 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCg                                            <  1:188222/129‑1 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCg                                            >  2:1132854/1‑129 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCg                                            <  1:1132854/129‑1 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCg                                            >  2:188222/1‑129 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAgc                                 >  1:839763/1‑140 (MQ=255)

                                                                                      aTCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAgc                                 >  2:629798/1‑140 (MQ=255)

                                                                                            tGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTAc                           >  1:545472/1‑140 (MQ=255)

                                                                                             ggCAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACg                          >  1:1196898/1‑140 (MQ=255)

                                                                                               cAAGTATTTCATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGt                        <  2:150248/140‑1 (MQ=255)

                                                                                                        cATCGCTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGaaa               >  1:744468/1‑140 (MQ=255)

                                                                                                             cTGGGAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAgcgc          >  2:1149063/1‑140 (MQ=255)

                                                                                                                ggAGTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCt       >  2:1147625/1‑140 (MQ=255)

                                                                                                                   gTCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCTgac    <  2:117446/140‑1 (MQ=255)

                                                                                                                    tCGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCTgacg   >  1:165572/1‑140 (MQ=255)

                                                                                                                     cGGGTCAGGCCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCTgacga  >  1:1043125/1‑140 (MQ=255)

ATTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGTCTGGATTTAAGTTCCATCCTTGATAGCCTCACCGCCGCGCAAAAAGCGACGCTAACCCCCATTTCAAATCAGCAATCGTCGTTTACCGCTAAACTTAGCGCCTACGGTACGCTGAAAAGCGCGCTGACGA  >  NC_000913/2003781‑2004037

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