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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,856,087	T→A	100%	P80P (CCT→CCA)	USA300HOU_2698 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,856,087	0	T	A	100.0%	80.9 / NA	27	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (9/18); total (9/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTCA  >  CP000730/2855970‑2856224

tAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAttt                                                                                                                    <  1:189455/141‑1 (MQ=255)

  aaGCTATATCAATACTGAAACAAGCTTTATTTCAGAACCAACTACATTTTAAAACGGAAGTTCGGTCATCATTACCTTTTACGTTAACTGGAGAGGAGCAATGCAATCATGCGCCAAAACGTCAACAAAGAGTAGAttttt                                                                                                                  >  2:37807/1‑140 (MQ=255)

    gctttgcgaaTACTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTGCCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTtata                                                                                                                <  2:57269/133‑1 (MQ=255)

     cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                               <  1:239366/141‑1 (MQ=255)

     cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                               >  1:34669/1‑141 (MQ=255)

      tataTCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgt                                                                                                              >  2:145373/1‑141 (MQ=255)

      tataTCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTAATAgt                                                                                                              >  1:149514/1‑141 (MQ=255)

          tCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAACGTTTTCTTTTATAgttgtt                                                                                                          <  2:2444/141‑1 (MQ=255)

                  ggAACAAGCTTTATTTCAGCCCCCACTATATTTTACGCCGGAACTCCCGGAAGCATTACCTGGTTAGTTGTCTGGAGATATGGCTTGCAAGCATGGGCCAAGACGGCAACAAATGATAGATTTTATAGTTGTTACagcagc                                                                                                  <  2:93859/141‑1 (MQ=255)

                    aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGcatcat                                                                                                >  2:240216/1‑141 (MQ=255)

                       aaGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAg                                                                                             <  1:42725/141‑1 (MQ=255)

                         gCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGat                                                                                           >  1:76044/1‑141 (MQ=255)

                                            tACATTTTAAAACGGACGTTCAGTCATCATTACCGTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCAc                                                                        <  1:9425/141‑1 (MQ=255)

                                              cATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                      >  1:197299/1‑141 (MQ=255)

                                                ttttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGt                                                                    <  1:240216/141‑1 (MQ=255)

                                                   tAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTac                                                                 <  2:193597/141‑1 (MQ=255)

                                                                 attcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATTCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttattt                                                   <  2:115697/139‑1 (MQ=255)

                                                                 aGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttattt                                                   <  1:141389/141‑1 (MQ=255)

                                                                      tcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTTACTGGTTACAACAGAATTTATTTGGTCt                                              <  1:182884/141‑1 (MQ=255)

                                                                          tACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCACCAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTTATTGGTCttgcc                                          >  1:233670/1‑137 (MQ=255)

                                                                            ccTTTGAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCt                                        <  2:203953/141‑1 (MQ=255)

                                                                                 tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg                                   >  1:75773/1‑141 (MQ=255)

                                                                                         cAGTAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACa                           <  1:84497/141‑1 (MQ=255)

                                                                                               aTGTGTCATGCACTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTTTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg                     <  1:132187/141‑1 (MQ=255)

                                                                                               aTGTGTCATGCAATCATGCACCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg                     <  1:260267/141‑1 (MQ=255)

                                                                                                                gcgcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAAtt    <  2:34669/141‑1 (MQ=255)

                                                                                                                  gcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATGCGGACCTCCAATATTAATTCa  <  1:145373/141‑1 (MQ=255)

TAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTCA  >  CP000730/2855970‑2856224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A