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
A9 F174 I0 R1	34	41.4	875437	98.7%	864056	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	100%	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,646,189	0	G	C	100.0%	119.0 / NA	37	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (19/18); total (19/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGAT  >  USA300TCH1516_ALE/1646053‑1646320

tttATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCttt                                                                                                                                 <  1:731417/141‑1 (MQ=255)

tttATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCttt                                                                                                                                 <  1:440675/141‑1 (MQ=255)

   aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTac                                                                                                                              >  1:183710/1‑141 (MQ=255)

     cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                            >  1:391743/1‑141 (MQ=255)

     cACTTGCAACACCATGTGGTAATGCACCACTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAACTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTATTTTTCAGTCATGCCTCCTTTTacac                                                                                                                            >  1:562316/1‑140 (MQ=255)

      tcTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaac                                                                                                                           <  1:332411/140‑1 (MQ=255)

      aCTTCCCACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaac                                                                                                                           <  1:225635/141‑1 (MQ=255)

       cTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaaca                                                                                                                          >  1:414403/1‑141 (MQ=255)

         tGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGt                                                                                                                        <  1:269994/141‑1 (MQ=255)

             acacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                                    <  1:819711/141‑1 (MQ=255)

                ccATGTGGTAATGCACCTCTATGACCAGGTGCTACAATCGTATCGAATGATGGTCCATGTGCTCCTATTTCTCGCATTTTGCTTTCTAATCTTGTCTTTAATTCTTTTTCTGTCATGCCTCTTTTTACACCAGTTAAAatt                                                                                                                 >  1:858661/1‑140 (MQ=255)

                ccATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAata                                                                                                                 >  1:468616/1‑141 (MQ=255)

                ccATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAAAAATGCCTTTAAGTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAata                                                                                                                 >  1:67290/1‑141 (MQ=255)

                     tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCTAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTTTTTTTTAGTCATGCCTCCTTTTACGACAGTTGAAATATATTc                                                                                                            >  1:363335/1‑141 (MQ=255)

                     tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTc                                                                                                            >  1:550350/1‑141 (MQ=255)

                            gCACCTCTATGACCAGTTGGTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTAAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGtt                                                                                                     >  1:486433/1‑141 (MQ=255)

                                     tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGTTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAACATATATTCATATGTTTTATcaaca                                                                                            >  1:203221/1‑141 (MQ=255)

                                     tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATcaaca                                                                                            >  1:141402/1‑141 (MQ=255)

                                               cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                  <  1:514569/141‑1 (MQ=255)

                                               cTACAATCGTATCGAATGATGGTCCAACTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                  <  1:530657/141‑1 (MQ=255)

                                               cTACAATCGTATCCAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                  <  1:851015/141‑1 (MQ=255)

                                                tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                                 >  1:843851/1‑141 (MQ=255)

                                                  cAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtt                                                                               >  1:693130/1‑141 (MQ=255)

                                                    tttttATCGAATGATGGTCCAGCTTCTCCGAATTCTTTCATTTTGCTTTCGTATATTGCCTTGATTTTTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                             <  1:390156/137‑1 (MQ=255)

                                                    aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                             <  1:8686/141‑1 (MQ=255)

                                                              atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                   <  1:173952/141‑1 (MQ=255)

                                                                           tGCTCCTAATTCTAGCATGTTGCATTCTAATATTGCCTTTAATTCTTTTTCAGTCATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGCATTAAAGCAATTCCGTCAGc                                                      <  1:548314/141‑1 (MQ=255)

                                                                                    ttCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                             <  1:790036/141‑1 (MQ=255)

                                                                                    ttCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                             <  1:573074/141‑1 (MQ=255)

                                                                                         gCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtctc                                        >  1:655331/1‑141 (MQ=255)

                                                                                            ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTCGCTGCTTGTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTaa                                     >  1:160329/1‑141 (MQ=255)

                                                                                                     cTAACATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTa                            <  1:734592/141‑1 (MQ=255)

                                                                                                           ttGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCACTTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACactgt                      >  1:78966/1‑137 (MQ=255)

                                                                                                           ttGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTCCAGTAt                      >  1:189595/1‑141 (MQ=255)

                                                                                                                             cAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg    >  1:653773/1‑141 (MQ=255)

                                                                                                                               gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat  <  1:653332/141‑1 (MQ=255)

                                                                                                                               gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat  <  1:581666/141‑1 (MQ=255)

TTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGAT  >  USA300TCH1516_ALE/1646053‑1646320

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A