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
A19 F50 I0 R1	80	46.5	1794022	91.0%	1632560	142.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,019,309	C→A	27.8%	D249Y (GAT→TAT)	ompA ←	outer membrane porin A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,019,309	0	C	A	27.8%	55.8 / 17.7	43	D249Y (GAT→TAT)	ompA	outer membrane porin A
Reads supporting (aligned to +/- strand): ref base C (18/13); new base A (7/5); total (25/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

GAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGAGC  >  NC_000913/1019167‑1019447

gagaTCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATc                                                                                                                                            >  2:128673/1‑143 (MQ=255)

agtaTCTTGTCTCCCGGGAGTCCTTTGGATATCAGGTAATAAATAACAGGCTGAGCACGGCGCTCGGACAGGCCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATc                                                                                                                                            <  2:614469/140‑1 (MQ=255)

  gaTTTTGTCGGGCGGGATGCCGTTGGGGACCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCa                                                                                                                                          <  2:570068/143‑1 (MQ=255)

     ctggTCTGCCGGGATGCCTTTGGGGATCAGGTAGTCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGATCCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGt                                                                                                                                       <  2:588993/140‑1 (MQ=255)

     ctcgccTGCCGGGATACCTTTGGAGATCAGGTAAGCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGt                                                                                                                                       <  1:93832/138‑1 (MQ=255)

             ccGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAgc                                                                                                                               <  1:837174/143‑1 (MQ=255)

                ggATACCTGTGGAGGTCAGGTAAGCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAgctgg                                                                                                                            <  2:847952/143‑1 (MQ=255)

                        ttGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTAAGGAACCGTCTTTCGGATACAGGTTGCTCAGATGGCTGTATAg                                                                                                                    >  1:482203/1‑143 (MQ=255)

                          ggAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCt                                                                                                                  <  1:20319/143‑1 (MQ=255)

                                catgTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCa                                                                                                            <  2:467475/140‑1 (MQ=255)

                                cAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCa                                                                                                            >  1:619031/1‑143 (MQ=255)

                                cAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGCACAGCTGATcgg                                                                                                            >  1:141360/1‑141 (MQ=255)

                                  gttattCAACAACAGTCTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCaga                                                                                                          <  2:813113/138‑1 (MQ=255)

                                  ggTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCaga                                                                                                          <  1:61732/143‑1 (MQ=255)

                                        caacaaCAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCCCCTGGCTGTCCAGCTGCTCCAGAGCAGcc                                                                                                    >  1:237704/1‑143 (MQ=255)

                                         aacaacAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGGTCCAGAGCAGCCt                                                                                                   >  2:702172/1‑143 (MQ=255)

                                         aacaacAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGCATCCAGGTTGCTCAGCTGGCTGTACAGCCGCTCCGGGgccgccg                                                                                                   >  2:708011/1‑142 (MQ=255)

                                                   tGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCgg                                                                                         >  1:143554/1‑143 (MQ=255)

                                                          ggCGCTCGGACACACCCTGGTTGTAAGCGTGAGACCCGATGCGGTCGGTGTAACCCAGAACGACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAgg                                                                                  <  2:804406/143‑1 (MQ=255)

                                                                 ggACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGTCTGACCTTCCGGTTTCAGGGTTGCtt                                                                           <  1:128673/143‑1 (MQ=255)

                                                                   aCAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGATttg                                                                         >  1:546731/1‑143 (MQ=255)

                                                                        cccTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTgttgaa                                                                    <  1:730513/143‑1 (MQ=255)

                                                                                    gCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAAc                                                        >  2:385068/1‑143 (MQ=255)

                                                                                      gTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCt                                                                                                   >  1:430638/1‑98 (MQ=255)

                                                                                      gTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCt                                                                                                   <  2:430638/98‑1 (MQ=255)

                                                                                        cAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCa                                                    >  1:397013/1‑143 (MQ=255)

                                                                                         aGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCCGCGCAGCCTGACCCTCCGGTTTCAGGGTTGCGTTGTTGAAGTTGAACAGAACGTCAg                                                   >  1:458578/1‑143 (MQ=255)

                                                                                         aGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTGGCTTTGTTGAAGATGCACAGAAcagcag                                                   >  2:495381/1‑138 (MQ=255)

                                                                                                       cggtGTATCTCAGATCAACTTCGGAACCGTCTTTCGGATACAGTTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAg                                     <  1:228471/143‑1 (MQ=255)

                                                                                                        ggtGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGt                                    >  2:494493/1‑143 (MQ=255)

                                                                                                            tAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCtt                                <  2:615999/143‑1 (MQ=255)

                                                                                                             aacggaGAACGACTACGGAACCGCCTGTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACGGAACGTCAGACTTCAGAGTGAAGTGCTTg                               <  1:872717/138‑1 (MQ=255)

                                                                                                              aCCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTgg                              >  2:616406/1‑143 (MQ=255)

                                                                                                               cccAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGGTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCGGACTTCAGGGTGAAGTGCTTGGt                             >  1:420494/1‑143 (MQ=255)

                                                                                                                ccAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAACAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTCGGTGGTGGACCGAACATCTGACCTCAGAGTGAAGTGCTTGGTc                            >  1:647258/1‑143 (MQ=255)

                                                                                                                        accgcGGACCCGTCTTGCGGTGCCGGGTTGCTCAGCTGGCTGCACAGCTGATCCAGAGCAGCCTGAGCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTc                    <  2:157314/139‑1 (MQ=255)

                                                                                                                         caagggAACCGTCTTTCGGAGACAGGTGGGTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTcc                   <  1:705869/139‑1 (MQ=255)

                                                                                                                         cTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAAGGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTcc                   >  1:363739/1‑143 (MQ=255)

                                                                                                                          tACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGAACCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCg                  >  1:193451/1‑143 (MQ=255)

                                                                                                                          tACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACGTGAGAGTGAAGTGCTTGGGCTCTCCTTCCg                  >  2:611669/1‑143 (MQ=255)

                                                                                                                                   gTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTAAGACATCAGAGTGAAGTGCTTGGTCTGTACTTGCGGTGCCGGAg         >  2:54885/1‑143 (MQ=255)

                                                                                                                                    tCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGc        >  1:825838/1‑143 (MQ=255)

                                                                                                                                        tCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGa    >  1:877597/1‑143 (MQ=255)

                                                                                                                                         cGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGCGCCGGAGCTGGAg   >  1:821671/1‑143 (MQ=255)

                                                                                                                                          ggATACAGGTTGCTCAGCTGGCTGTAAAGCTGAACCAGAGCAGCCTGACCTTCCGGTTTCAGGGATGCGTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCAGTGGCGGAGAGGGAGc  >  2:379492/1‑143 (MQ=255)

GAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGAGC  >  NC_000913/1019167‑1019447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A