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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	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%	160.3 / NA	46	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (23/23); total (23/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646057‑1646325

tCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTaca                                                                                                                                    <  1:236083/141‑1 (MQ=255)

   cTTGCAACACCATGTGGTAATGAACCTCTATGACCAGATGATACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaaca                                                                                                                                 >  1:449731/1‑141 (MQ=255)

             cATGTGGTAATGCACCGCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGGTAAAatat                                                                                                                       >  1:304848/1‑141 (MQ=255)

              aTGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAataaa                                                                                                                      >  1:275823/1‑139 (MQ=255)

                gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATAtt                                                                                                                    >  2:222457/1‑141 (MQ=255)

                gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATAtt                                                                                                                    >  1:510992/1‑141 (MQ=255)

                gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATAtt                                                                                                                    <  2:273553/141‑1 (MQ=255)

                 tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCGTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACGACAGTTAAAATATGTTc                                                                                                                   >  2:409540/1‑141 (MQ=255)

                      aggCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                              <  2:457947/139‑1 (MQ=255)

                      aTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                              >  2:174023/1‑141 (MQ=255)

                      aTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                              >  2:226280/1‑141 (MQ=255)

                             tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcatc                                                                                                       <  1:6631/141‑1 (MQ=255)

                                     cAGATGCGACAATCGTATCGAATGATGGTCCAGCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAatat                                                                                               <  2:166813/141‑1 (MQ=255)

                                       gATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCCACAATATTa                                                                                             >  2:249717/1‑141 (MQ=255)

                                          gCTACAATCGTATCGACTGATGCTTGAGCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgct                                                                                          >  2:131544/1‑141 (MQ=255)

                                           cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                         <  1:169012/141‑1 (MQ=255)

                                           cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTATCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                         <  1:455818/141‑1 (MQ=255)

                                            tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                                        <  2:449731/141‑1 (MQ=255)

                                             acacTCGTCTCGAATGCTGGTCCATCTGCTCCTACTACTAGCATCTTGCCTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACCACAGTTAAAATATATTCATGTGTTTCCTCAACAATATCAgctgct                                                                                       >  2:164710/1‑141 (MQ=255)

                                              cAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtt                                                                                      >  1:423512/1‑141 (MQ=255)

                                                aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTCAACTGTCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                                    <  1:570745/141‑1 (MQ=255)

                                                aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                                    <  1:418643/141‑1 (MQ=255)

                                                    tATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGaa                                                                                >  1:361737/1‑141 (MQ=255)

                                                       cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTa                                                                             >  2:228866/1‑141 (MQ=255)

                                                        gAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTaa                                                                            <  2:118786/141‑1 (MQ=255)

                                                                  ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCg                                                                  >  2:269377/1‑141 (MQ=255)

                                                                       tGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGc                                                           >  1:500639/1‑141 (MQ=255)

                                                                         cTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCAt                                                         >  1:168659/1‑141 (MQ=255)

                                                                           ccTAATTTTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCt                                                       <  1:71501/141‑1 (MQ=255)

                                                                            cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTATCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCtt                                                      <  2:502387/141‑1 (MQ=255)

                                                                              aaTTCTAGCCTTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAGTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTg                                                    <  1:417634/141‑1 (MQ=255)

                                                                              aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATGCTTATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTg                                                    <  1:82966/141‑1 (MQ=255)

                                                                                  cTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGt                                                >  2:35596/1‑141 (MQ=255)

                                                                                          ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAAtt                                        <  1:174023/141‑1 (MQ=255)

                                                                                            gCTTTCTAATATTGCCTTTAATTCTTTTTCAGACATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTTGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAAtttt                                      <  1:409540/141‑1 (MQ=255)

                                                                                              tttCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTAt                                    <  2:149512/141‑1 (MQ=255)

                                                                                                    atatTGCCCTTGATTCTTTTTTAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCCGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAg                              <  1:106008/141‑1 (MQ=255)

                                                                                                         gCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTGTCTAATTTTATCTACAGTATTa                         >  1:74927/1‑141 (MQ=255)

                                                                                                         gCCTTTAATTCTTTTTCAGTCATGCCACCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTa                         >  2:366705/1‑141 (MQ=255)

                                                                                                               aaTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg                   <  1:363182/141‑1 (MQ=255)

                                                                                                                 ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt                 <  1:272396/141‑1 (MQ=255)

                                                                                                                    tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAG‑‑ATTACGCTGCATCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat              >  1:17493/1‑141 (MQ=255)

                                                                                                                     ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttatt             >  1:477224/1‑141 (MQ=255)

                                                                                                                          aGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGa        <  1:131544/141‑1 (MQ=255)

                                                                                                                           gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat       >  1:490577/1‑141 (MQ=255)

                                                                                                                                gCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACg  <  2:168659/141‑1 (MQ=255)

TCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCG‑T‑CAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646057‑1646325

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