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
A8 F1 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,504,006	G→A	intergenic (‑575/‑52)	insG ← / → yjhB	IS4 transposase/putative MFS transporter, membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,504,006	0	G	A	100.0%	138.5 / NA	44	intergenic (‑575/‑52)	insG/yjhB	IS4 transposase/putative MFS transporter, membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (21/23); total (21/23)

CATAGAGTGAAATATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGGCTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCATGGCT  >  NC_000913/4503887‑4504122

cATAGAGTGAAATATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTa                                                                                                   <  1:693076/139‑1 (MQ=255)

     agTGAAATATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGc                                                                                              <  1:831496/139‑1 (MQ=255)

       tGAAATATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCta                                                                                            >  1:194621/1‑139 (MQ=255)

         aaaTATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCtata                                                                                          >  1:389391/1‑139 (MQ=255)

               gTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACttt                                                                                                    >  1:1045047/1‑123 (MQ=255)

               gTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACttt                                                                                                    <  2:1045047/123‑1 (MQ=255)

                                          tACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAg                                                         <  2:389391/139‑1 (MQ=255)

                                          tACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAg                                                         <  2:194621/139‑1 (MQ=255)

                                               aTTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAggg                                                                                               <  2:911970/96‑1 (MQ=255)

                                               aTTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAggg                                                                                               >  1:911970/1‑96 (MQ=255)

                                               aTTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGc                                                                                              <  1:134150/97‑1 (MQ=255)

                                               aTTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGc                                                                                              >  2:134150/1‑97 (MQ=255)

                                                  aGGTATTGATAACAATCAATAGTATTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        >  1:1962/1‑132 (MQ=255)

                                                  aGGTATTGATAACAATCAATAGTATTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        >  1:310717/1‑132 (MQ=255)

                                                  aGGTATTGATAACAATCAATAGTATTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        <  2:1962/132‑1 (MQ=255)

                                                  aGGTATTGATAACAATCAATAGTATTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        <  2:310717/132‑1 (MQ=255)

                                                         gATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAg                                                                            <  1:665734/105‑1 (MQ=255)

                                                         gATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAg                                                                            >  2:665734/1‑105 (MQ=255)

                                                           tAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGt                                                   <  1:928359/128‑1 (MQ=255)

                                                           tAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGt                                                   >  2:928359/1‑128 (MQ=255)

                                                                 tcaatAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAggg                                                                                               <  1:454132/78‑1 (MQ=255)

                                                                 tcaatAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAggg                                                                                               >  2:454132/1‑78 (MQ=255)

                                                                 tcaatAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGc                                                                                              >  1:921186/1‑79 (MQ=255)

                                                                 tcaatAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGc                                                                                              <  2:921186/79‑1 (MQ=255)

                                                                    atAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATccacca                               >  1:167062/1‑139 (MQ=255)

                                                                         aCTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATaa                                                                                 <  2:797876/84‑1 (MQ=255)

                                                                         aCTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATaa                                                                                 >  1:797876/1‑84 (MQ=255)

                                                                           tGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGa                        >  2:125176/1‑139 (MQ=255)

                                                                             gCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTa                                                                                                   >  1:1263950/1‑62 (MQ=255)

                                                                             gCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTa                                                                                                   <  2:1263950/62‑1 (MQ=255)

                                                                             gCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGaaa                      >  1:13900/1‑139 (MQ=255)

                                                                              cGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCa                                                       <  1:264384/105‑1 (MQ=255)

                                                                              cGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCa                                                       >  2:264384/1‑105 (MQ=255)

                                                                                         actatatTATTATTTCTGGATATTGTTGAGACTCCCTAAGATTTACTTTAAGAGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCAATGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTcc          <  2:30499/136‑1 (MQ=255)

                                                                                            atatAATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCa       <  2:167062/139‑1 (MQ=255)

                                                                                             tataATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        <  2:53949/89‑1 (MQ=255)

                                                                                             tataATTATTTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGc                                                        >  1:53949/1‑89 (MQ=255)

                                                                                                 attattTCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCATGGCt  <  1:125176/139‑1 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCa                                                       >  2:1247115/1‑80 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCa                                                       <  1:1247115/80‑1 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGt                                         <  2:1143077/94‑1 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGt                                         >  1:1143077/1‑94 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTAAATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCa       <  2:1205164/128‑1 (MQ=255)

                                                                                                       tCTGGATATTGTTGAGACTCCCTAATATTTACTTTAAGGGCTAAATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCa       >  1:1205164/1‑128 (MQ=255)

CATAGAGTGAAATATGTTAAGAAGAAATGGAGGAAAAGATTGTACTGATTAGGTATTGATAACAATCAATAGTACTGGCGTATTTGAAGACAATATAATTATTTCTGGATATTGTTGAGGCTCCCTAATATTTACTTTAAGGGCTATATTAGAATAACACAGGAAACAAATATGGCAACAGCATGGTATAAACAAGTTAATCCACCACAACGGAAAGCTCTTTTTTCCGCATGGCT  >  NC_000913/4503887‑4504122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A