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 F18 I0 R1	80	28.1	641476	93.5%	599780	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%	73.4 / NA	27	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (14/13); total (14/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855951‑2856220

agaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGTGCCaaaa                                                                                                                                    <  2:231690/140‑1 (MQ=255)

    gCATGGCGTTGGTCCTAAAGCTATATCAATATTGGACCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTc                                                                                                                                <  2:66292/140‑1 (MQ=255)

        ggCGTTAATCCTAAAGCTATATCAATGTAGGAACAAGCTTTATTTCATCACCAACTACATTTTAAAACGGAAGTTCAGTCATCGTTACCTTTTAAGTTAAAAGGCGATGTCTCATGCCATCATGCGCCAAAAAGtacaca                                                                                                                            >  2:122595/1‑135 (MQ=255)

                    aatgCTATATCAATAGTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAGGCATGCGCCAAAACGTCAACAAATGATAGGttt                                                                                                                <  2:292374/137‑1 (MQ=255)

                             tCAATATTGGAAAAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                       <  2:75236/140‑1 (MQ=255)

                               aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACTGAAGTTCAGTCATCATTACCTTTTAAGTGAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  2:16125/140‑1 (MQ=255)

                               aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  1:188958/140‑1 (MQ=255)

                               aaTATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTa                                                                                                     <  1:34551/140‑1 (MQ=255)

                                    tGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagca                                                                                                >  2:162901/1‑140 (MQ=255)

                                              tttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGata                                                                                      >  1:128871/1‑140 (MQ=255)

                                                 aTTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg                                                                                   >  1:272805/1‑140 (MQ=255)

                                                          ccAACTACTTTTTAAATCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTAc                                                                          <  1:56586/140‑1 (MQ=255)

                                                                  aTTTTAAAACGGAAGTTCAGTCATCATTACCTCTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                  <  2:22693/140‑1 (MQ=255)

                                                                      tAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGTGGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTGCCTGGTTa                                                              >  2:240702/1‑140 (MQ=255)

                                                                        aaaCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGAGGTGTCATGCAATCATGCTCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTaca                                                            >  2:76437/1‑140 (MQ=255)

                                                                           cGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAGTATTACGTTCATTGGtagaaaca                                                         >  2:191451/1‑133 (MQ=255)

                                                                                         tcatTACCTGTTCAGTGAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc                                           <  1:302862/140‑1 (MQ=255)

                                                                                            ttACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGt                                        >  1:291887/1‑140 (MQ=255)

                                                                                                        ttAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCtt                            >  1:72094/1‑140 (MQ=255)

                                                                                                          aaCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCTCTTTg                          >  1:291010/1‑140 (MQ=255)

                                                                                                               gagaTGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACata                     <  2:183318/140‑1 (MQ=255)

                                                                                                                   tgtgTCATGCAATCAAGCGCCAACACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGACATTGAATTCTTACGTTTACTGGTTACAACAGAATTAATTAGGTCTGTCCCTGGCCGCTTTGAAATATACg                 >  2:65919/1‑140 (MQ=255)

                                                                                                                     tgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGa               >  1:31543/1‑140 (MQ=255)

                                                                                                                               tCATGCGCCAAAACGTTAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat     <  1:126102/140‑1 (MQ=255)

                                                                                                                                cATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAAtttt    >  1:142737/1‑140 (MQ=255)

                                                                                                                                 aTGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTa   <  1:75023/140‑1 (MQ=255)

                                                                                                                                  tGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGCATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  >  1:90421/1‑140 (MQ=255)

                                                                                                                                  tGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  <  1:145276/140‑1 (MQ=255)

AGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855951‑2856220

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