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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	582,152	C→T	pseudogene (653/653 nt)	ybcY ←	pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	582,152	0	C	T	100.0%	174.4 / NA	54	pseudogene (653/653 nt)	ybcY	pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (30/24); total (30/24)

GTGTTGCTGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTTGGATGCTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTT  >  NC_000913/582026‑582280

gtgtTGCTGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTg                                                                                                                     <  2:911148/139‑1 (MQ=255)

       tGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGa                                                                                                              <  2:400699/139‑1 (MQ=255)

          aCCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTATTTTTTTTCCTGAAGCGGaaa                                                                                                            >  2:581985/1‑139 (MQ=255)

              tgtTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACAtt                                                                                                       >  1:247061/1‑139 (MQ=255)

                         cAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTAcc                                                                                            >  2:933892/1‑139 (MQ=255)

                          aaCTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCt                                                                                           >  1:125202/1‑139 (MQ=255)

                               cACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATtacta                                                                                                   >  1:432421/1‑126 (MQ=255)

                               cACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATtacta                                                                                                   <  2:432421/126‑1 (MQ=255)

                               cACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAAc                                                                                      >  1:53785/1‑139 (MQ=255)

                                       atTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGttt                                                                              >  2:83204/1‑139 (MQ=255)

                                                ccTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATtct                                                                     >  1:956850/1‑139 (MQ=255)

                                                     gAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTg                                                                                                                     <  1:37606/86‑1 (MQ=255)

                                                     gAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTg                                                                                                                     >  2:37606/1‑86 (MQ=255)

                                                          cTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCt                                                                                    <  2:49263/114‑1 (MQ=255)

                                                          cTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCt                                                                                    >  1:49263/1‑114 (MQ=255)

                                                             tCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACTTTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTga                                                        <  1:1011092/139‑1 (MQ=255)

                                                              cAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 <  2:972478/97‑1 (MQ=255)

                                                              cAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 >  1:972478/1‑97 (MQ=255)

                                                              cAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTgag                                                       <  1:933892/139‑1 (MQ=255)

                                                                    gTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGtata                                                 <  1:1114251/139‑1 (MQ=255)

                                                                     tAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTatat                                                <  2:53785/139‑1 (MQ=255)

                                                                      aaTCATTGGGTCTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAAAATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATAtg                                               >  2:267891/1‑139 (MQ=255)

                                                                       aTCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATAtgt                                              >  1:366519/1‑139 (MQ=255)

                                                                             gggATTATGCCGCAGTACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAg                                        >  2:421283/1‑139 (MQ=255)

                                                                             gggATTATGCCGCAGCACGTCTTACGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             >  2:753992/1‑70 (MQ=255)

                                                                             gggATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             <  1:753992/70‑1 (MQ=255)

                                                                                    tGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 >  1:773379/1‑75 (MQ=255)

                                                                                    tGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 <  2:773379/75‑1 (MQ=255)

                                                                                    tGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCcttctt                                 >  1:38577/1‑139 (MQ=255)

                                                                                         cagcaCGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             <  1:830762/58‑1 (MQ=255)

                                                                                         cagcaCGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             >  2:830762/1‑58 (MQ=255)

                                                                                         cagcaCGTCTTAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGaa                            >  2:1011118/1‑139 (MQ=255)

                                                                                                  ttAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 <  2:73734/61‑1 (MQ=255)

                                                                                                  ttAAGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACa                                                                                                 >  1:73734/1‑61 (MQ=255)

                                                                                                    aaGCAAGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGtt                 <  1:614725/139‑1 (MQ=255)

                                                                                                         aGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaaaa                                                                                                           <  2:708038/44‑1 (MQ=37)

                                                                                                         aGAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaaaa                                                                                                           >  1:708038/1‑44 (MQ=37)

                                                                                                          gAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTaa                                                                           <  1:700238/75‑1 (MQ=255)

                                                                                                          gAACATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTaa                                                                           >  2:700238/1‑75 (MQ=255)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             <  2:591782/40‑1 (MQ=25)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGaa                                                                                                             >  1:591782/1‑40 (MQ=25)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGt                                                                                               >  2:594110/1‑54 (MQ=38)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGt                                                                                               <  1:594110/54‑1 (MQ=38)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTgag                                                       >  2:256098/1‑94 (MQ=255)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTgag                                                       <  1:256098/94‑1 (MQ=255)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAg          >  2:489123/1‑139 (MQ=255)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAg          >  1:425480/1‑139 (MQ=255)

                                                                                                           aaCATGCTGCGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAg          >  1:1033885/1‑139 (MQ=255)

                                                                                                                gctgcGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGctct                                                          <  1:264008/86‑1 (MQ=255)

                                                                                                                gctgcGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGctct                                                          >  2:264008/1‑86 (MQ=255)

                                                                                                                 ctgcGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCt    >  2:968069/1‑139 (MQ=255)

                                                                                                                   gcGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCttt  <  2:425480/139‑1 (MQ=255)

                                                                                                                   gcGGTT‑GATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCGTCGGAATCTTTTGTGTTTGAAAAGATGCCttt  <  1:1011118/139‑1 (MQ=255)

                                                                                                                    gctgttgATGTTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCttt  <  1:267891/133‑1 (MQ=255)

GTGTTGCTGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTTGGATGCTA‑TTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTT  >  NC_000913/582026‑582280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A