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
A12 F1 I1 R1	65	25.3	1027584	98.0%	1007032	120.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,554,430	(T)_7→8	intergenic (+69/‑146)	uxuB → / → uxuR	D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor, autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,554,423	1	.	T	100.0%	107.3 / NA	32	intergenic (+62/‑153)	uxuB/uxuR	D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor, autorepressor
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (16/16); total (16/16)

GGCGGCATATCAGCAGCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCG‑TTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAAAATTTGA  >  NC_000913/4554304‑4554548

ggcggcATATCAGCAGCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTa                                                                                                             <  1:416533/139‑1 (MQ=255)

      atatCAGCAGCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACCTGcc                                                                                                       <  1:283586/139‑1 (MQ=255)

       tatCAGCAGCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCa                                                                                                      <  2:483316/139‑1 (MQ=255)

          cagcagCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACt                                                                                                   >  1:132261/1‑139 (MQ=255)

                  gtgCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGc                                                                                           <  2:165879/139‑1 (MQ=255)

                  gtgCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGc                                                                                           >  2:117974/1‑139 (MQ=255)

                    gCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTa                                                                                         <  1:117974/139‑1 (MQ=255)

                         cgcgGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGt                                                                                    <  1:180622/139‑1 (MQ=255)

                         cgcgGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGt                                                                                    <  2:176442/139‑1 (MQ=255)

                             gTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAg                                                                                >  2:213637/1‑139 (MQ=255)

                                  cgcgAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTCCAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             <  1:302956/121‑1 (MQ=255)

                                  cgcgAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             <  1:204927/121‑1 (MQ=255)

                                  cgcgAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             >  2:302956/1‑121 (MQ=255)

                                  cgcgAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             >  2:204927/1‑121 (MQ=255)

                                          tgtgGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACg                                                                   >  2:470217/1‑139 (MQ=255)

                                            tgGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACggg                                                                 <  2:502872/139‑1 (MQ=255)

                                                      gTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTaaaa                                                       >  1:241073/1‑139 (MQ=255)

                                                       taactaacTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAAt                                                      >  2:22803/1‑139 (MQ=255)

                                                               tGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGtt                                              >  2:348496/1‑139 (MQ=255)

                                                                   tACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             <  1:110942/88‑1 (MQ=255)

                                                                   tACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             >  2:110942/1‑88 (MQ=255)

                                                                             aCTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGta                                                                                   >  2:18876/1‑88 (MQ=255)

                                                                             aCTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGta                                                                                   <  1:18876/88‑1 (MQ=255)

                                                                               ttACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGTTGTAGGCCGGATAAGGc                              >  1:192498/1‑139 (MQ=255)

                                                                                         atcaaACTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGTTGTAGGCCGGATAAGGCGTTCAcgccg                    >  2:394620/1‑139 (MQ=255)

                                                                                             aaCTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGcc                                                                                                       >  2:306997/1‑52 (MQ=255)

                                                                                             aaCTGATATTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGcc                                                                                                       <  1:306997/52‑1 (MQ=255)

                                                                                                  atatTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACggg                                                                 >  2:38652/1‑85 (MQ=255)

                                                                                                  atatTTGGTTGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACggg                                                                 <  1:38652/85‑1 (MQ=255)

                                                                                                           tGACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAAAATTTGa  <  1:470217/139‑1 (MQ=255)

                                                                                                            gACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             >  2:250656/1‑47 (MQ=255)

                                                                                                            gACCAGTTTTCGTTTTTTTTGCCCACCTGTACGTGCCAACTTCCAGt                                                                                             <  1:250656/47‑1 (MQ=255)

GGCGGCATATCAGCAGCTGTGCGAACGCGGTGCGCGCGAGTGTGTGGCTGCGCTGTAACTAACTGATTACCCTACAGACTTACTGGTCAATCAAACTGATATTTGGTTGACCAGTTTTCG‑TTTTTTTGCCCACCTGTACGTGCCAACTTCCAGTGCTAATGGTATAGTTTGAGATTAACGGGGGCCGTAAAATTGCCCGTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAAAATTTGA  >  NC_000913/4554304‑4554548

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A