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 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

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%	92.6 / ‑6.5	33	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base A (15/16); minor base C (0/1); total (16/17)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATT  >  CP000730/2855952‑2856222

gaTGTATGGCGTTTGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAAc                                                                                                                                     <  1:118336/140‑1 (MQ=255)

   gCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGACAAAACGTc                                                                                                                                  >  2:335879/1‑140 (MQ=255)

    cATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTca                                                                                                                                 >  1:355407/1‑140 (MQ=255)

          gTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCACAACGTCAACaaaa                                                                                                                           >  1:162997/1‑139 (MQ=255)

            tGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                         >  2:350701/1‑140 (MQ=255)

                 cTAAAGTTATTTCAATATTGGAACTAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAt                                                                                                                    <  1:105441/140‑1 (MQ=255)

                        tataTCAATATTGGAACAAGATTTATTTCAGAACCAACTAAATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAAAAGGGGATGTGTCATGTAGTCATGCGCTGGTCCGTTAACAAATGATGGTTTTTGTAg                                                                                                             >  2:334422/1‑140 (MQ=255)

                          tatCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgtt                                                                                                           >  1:225186/1‑140 (MQ=255)

                             cAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgtt                                                                                                        >  2:325703/1‑140 (MQ=255)

                               atatTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGACGTTCAGTAATCCTTCCCTTTTAAGTTAACCGGAGATGTGTCATGCAATCATGCGCAAACACATCTACAAATGAGAGATTTTATAGTTGTTAc                                                                                                      >  2:336715/1‑140 (MQ=255)

                                 atTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCTGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcag                                                                                                    <  2:188035/140‑1 (MQ=255)

                                  ttGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagc                                                                                                   <  1:165832/140‑1 (MQ=255)

                                        cAAGCTATACTTCAACATCAACTGCATTTTAAAACGGAAGCTCAGTCATCATTACCTTCTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAtt                                                                                             >  2:254701/1‑140 (MQ=255)

                                                aTTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg                                                                                     <  1:907/140‑1 (MQ=255)

                                                          cAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAACGAGAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACg                                                                           <  1:335879/140‑1 (MQ=255)

                                                                               gTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatg                                                      >  2:125252/1‑139 (MQ=255)

                                                                                    ttcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttattt                                                 <  1:308204/139‑1 (MQ=255)

                                                                                        tcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc                                             <  1:189476/140‑1 (MQ=255)

                                                                                              ccTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTccc                                       <  2:354778/140‑1 (MQ=255)

                                                                                                  tttagacaaCAGTGGATGTGTCATGCAATCATGCGCCAAAACGTCAACAACTCACAGATCTGACAGGGGTGACAGCATCAGTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTAGTTGGTCTGTCCCTGGc                                   <  2:214857/133‑1 (MQ=255)

                                                                                                  ttACGTTAACATGAGAGGTGTCATGCAGTCAGGCGCCCATACGTCAACAAATGATATATTTTATCGTTGTTACATCAGCACGAGACACTAAATTATTACCATCACTGGTTACAACAGAATTTATTTTGTCAGTccttagc                                   <  2:160192/140‑6 (MQ=255)

                                                                                                   tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGcc                                  <  2:237843/140‑1 (MQ=255)

                                                                                                   tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGcc                                  <  2:158581/140‑1 (MQ=255)

                                                                                                       ttAACAGGGGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCtt                              <  1:144387/140‑1 (MQ=255)

                                                                                                         aaCAGGAGATGTGTCATGCAATCATTCGCCAAAACGTCAACAAATGATAGATTTTATGGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTg                            >  2:57290/1‑140 (MQ=255)

                                                                                                         aaCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTAGAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTg                            >  2:286501/1‑140 (MQ=255)

                                                                                                          aCAGGAGATGTGTCATGCAATCATGCGCCAAAGCGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGa                           <  2:309377/140‑1 (MQ=255)

                                                                                                           cAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGAc                          <  2:355407/140‑1 (MQ=255)

                                                                                                                     gtCATACAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGAc                >  1:342134/1‑140 (MQ=255)

                                                                                                                          gCAATCATGCGCCATAACGTCAACAAATGGTAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCaa           >  1:190484/1‑140 (MQ=255)

                                                                                                                             aTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCACAATTATATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAata        <  1:334422/140‑1 (MQ=255)

                                                                                                                               cATGCGACAGAACGTCAACAAATAATCGTCAGTATAGTTGATACAGCAGCATTAGATATTGAATTAGTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCATTGACATATACGGACCTCAAATAtt      >  1:262088/1‑140 (MQ=255)

                                                                                                                                   cgcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAAtt  >  1:197300/1‑140 (MQ=255)

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATT  >  CP000730/2855952‑2856222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A