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
A17 F57 I0 R1	30	26.7	570066	96.5%	550113	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%	95.7 / NA	30	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (15/15); total (15/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTA  >  CP000730/2855952‑2856219

gaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACg                                                                                                                                 >  1:202255/1‑141 (MQ=255)

      tGGCGTTGGTCCTAAAGCTATATCAATATGGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTACCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaaca                                                                                                                           <  2:259529/141‑1 (MQ=255)

       ggCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGCTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaacaa                                                                                                                          >  2:145403/1‑141 (MQ=255)

           ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                      <  1:275192/141‑1 (MQ=255)

           ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                      <  1:172193/141‑1 (MQ=255)

                       cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGTGATGTGTCATGCAATCATGCGCCAAAACGTCCACAAATGATAGATTTTATAg                                                                                                          <  1:173490/141‑1 (MQ=255)

                           atCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                      >  2:13264/1‑141 (MQ=255)

                               atatTGGAACAAGCTTTATTTCAGCACCAACTACATCTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAca                                                                                                  <  2:14794/141‑1 (MQ=255)

                                       aCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAtt                                                                                          >  2:93995/1‑141 (MQ=255)

                                        cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAAACATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTa                                                                                         <  1:183838/141‑1 (MQ=255)

                                        cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAAACATGCGCCAAAACGTCAACAAATGAGAGATTTTATAGTTGTTACAGCAGCATTa                                                                                         <  1:183837/141‑1 (MQ=255)

                                          tgcgttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCCTGCAATCATGCGCCAAAACGTCAACACATGATAGCTTTTATAGTTGTTACATCAGCATTAGa                                                                                       >  2:260801/5‑141 (MQ=255)

                                          aGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGa                                                                                       >  2:40499/1‑141 (MQ=255)

                                                      gCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattatt                                                                           >  1:139918/1‑141 (MQ=255)

                                                       cACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAttatta                                                                          <  1:13264/141‑1 (MQ=255)

                                                       cACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAttatta                                                                          >  2:168398/1‑141 (MQ=255)

                                                              tACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCAc                                                                   <  1:133166/141‑1 (MQ=255)

                                                               tcgtcttaacgcGGAAGCTCAGTCCACATTTACTTTTAAATTACCATGGGATTTGCGATGCAATCATGCGCCAAGTCGTCAACTAATGATAGATTTTCTTGTTGTTACAGCAGCATTAGATATTTAATTATTACGTTCACt                                                                  <  2:21466/130‑1 (MQ=255)

                                                                       aaaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAAGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTacaa                                                          >  1:268166/1‑141 (MQ=255)

                                                                        aaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTGGTTAAAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTccaac                                                         >  1:40911/1‑141 (MQ=255)

                                                                          cGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAg                                                       <  1:164978/141‑1 (MQ=255)

                                                                            gAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGaa                                                     >  1:260538/1‑141 (MQ=255)

                                                                                         catTACCTTTTAAGTTAACGAGAGATGTGTCATGCAATCATGCGCCAAAACGTCGACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTg                                        >  1:184573/1‑141 (MQ=255)

                                                                                             aCCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATAAGAGATTGTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGGTCACTGGTTACAACAGAATTTATTTGGTCTGTccc                                    >  1:66023/1‑141 (MQ=255)

                                                                                                ttttAAGTTAACAGGAGATGTGGCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTgg                                 <  2:240009/141‑1 (MQ=255)

                                                                                                   tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg                              <  1:93995/141‑1 (MQ=255)

                                                                                                          aCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGAc                       >  2:76698/1‑141 (MQ=255)

                                                                                                                            aaTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCCGCGTTTGATATTGAATTATTACTTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAata     <  1:266344/141‑1 (MQ=255)

                                                                                                                             aTCATGCGCCAAAACGTCAACAAACGATAGATTTTAAAGTTGTTACAGCAGCATTAGATATTGCATCACTAGCTGCACGGGTTTACACATAGTTTTTTTTGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat    <  1:280312/141‑1 (MQ=255)

                                                                                                                               cATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTa  >  1:213141/1‑141 (MQ=255)

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTA  >  CP000730/2855952‑2856219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A