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 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,521,593	C→T	295 (TAG→TAA)	xapR ←	transcriptional activator of xapAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,521,593	0	C	T	100.0%	102.4 / NA	32	295 (TAG→TAA)	xapR	transcriptional activator of xapAB
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/13); total (19/13)

ACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTA  >  NC_000913/2521481‑2521727

accaATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTAGTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCtt                                                                                                              >  1:675515/1‑139 (MQ=255)

  caATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTaa                                                                                                            >  2:994549/1‑139 (MQ=255)

       tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                       >  2:816523/1‑139 (MQ=255)

                 cccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCa                                                                                             >  2:432347/1‑139 (MQ=255)

                                     tATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         <  1:816523/139‑1 (MQ=255)

                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGCGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      >  1:157818/1‑106 (MQ=255)

                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGCGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      <  2:157818/106‑1 (MQ=255)

                                               ttGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCAATTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCAGGCGTCATCTGCTGTGTTTCATAAACAATATATAAAt                                                               <  2:675515/139‑1 (MQ=255)

                                                 gCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                              <  1:681993/122‑1 (MQ=255)

                                                 gCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                              >  2:681993/1‑122 (MQ=255)

                                                   gAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGc                                                           >  1:352950/1‑139 (MQ=255)

                                                        tGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGa                                                      <  2:352950/139‑1 (MQ=255)

                                                             gATGCGCTTCACTTAGCAGACTATTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTgtgt                                                                                   <  1:20501/105‑1 (MQ=255)

                                                             gATGCGCTTCACTTAGCAGACTATTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTgtgt                                                                                   >  2:20501/1‑105 (MQ=255)

                                                                 cgcTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGtt                                             >  1:1005837/1‑139 (MQ=255)

                                                                     tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAg                                         <  1:755293/139‑1 (MQ=255)

                                                                             cAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         >  1:87257/1‑99 (MQ=255)

                                                                             cAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         <  2:87257/99‑1 (MQ=255)

                                                                                actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCaa                                                                                                                    >  1:906252/1‑53 (MQ=255)

                                                                                actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCaa                                                                                                                    <  2:906252/53‑1 (MQ=255)

                                                                                actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                              >  2:639432/1‑139 (MQ=255)

                                                                                 ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             >  1:32980/1‑139 (MQ=255)

                                                                                     taTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      <  1:650791/62‑1 (MQ=255)

                                                                                     taTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      >  2:650791/1‑62 (MQ=255)

                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGcc                  >  1:770892/1‑139 (MQ=255)

                                                                                               aaTTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         >  1:376/1‑81 (MQ=255)

                                                                                               aaTTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         <  2:376/81‑1 (MQ=255)

                                                                                                   ccTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGc                   <  2:775724/131‑1 (MQ=255)

                                                                                                   ccTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGc                   >  1:775724/1‑131 (MQ=255)

                                                                                                            tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             >  1:770716/1‑112 (MQ=255)

                                                                                                            tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             <  2:770716/112‑1 (MQ=255)

                                                                                                            tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTa  >  1:266523/1‑139 (MQ=255)

ACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTA  >  NC_000913/2521481‑2521727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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