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
A13 F55 I0 R1	26	48.4	1146576	93.4%	1070901	139.9

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%	113.2 / NA	37	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (17/20); total (17/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGA  >  USA300TCH1516_ALE/1646059‑1646319

acgtGCAACACCATGTGGTAATGCACCTCTATGACCAGTTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                           <  2:53391/137‑1 (MQ=255)

aCTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                           >  1:217178/1‑140 (MQ=255)

 cTTGCAACCCCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaac                                                                                                                          <  2:36286/140‑1 (MQ=255)

      aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTa                                                                                                                     >  1:391636/1‑140 (MQ=255)

       acacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                                    >  1:171905/1‑140 (MQ=255)

                gttAATGCACCTCTATGCCCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTc                                                                                                           <  2:237446/138‑1 (MQ=255)

                 gTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTCATTCTAGCATTTTGCTTTCTAATCTTGCCTTTAATTCTTTTTCAGTCATTCCTCCTTTTACAACAGTTACAATTTATTCa                                                                                                          >  2:3852/1‑140 (MQ=255)

                       cACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGtt                                                                                                    <  2:310279/140‑1 (MQ=255)

                                  ccAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCATAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACATTTAAATTACATTCATATGATTCAACAACCat                                                                                         >  2:382730/1‑140 (MQ=255)

                                   cAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGCCATGCCTCATTTTACAACATTCAAGATATATTCATGAGTTTCATccacgcta                                                                                        >  2:194413/1‑136 (MQ=255)

                                    aGATGCTACAACCGTATTGAATGATGGGTCATCTTCTGCTAATTCTACCATTTTGCTCTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAatat                                                                                       <  2:400929/140‑1 (MQ=255)

                                           aCAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                                <  2:247304/140‑1 (MQ=255)

                                              aTCGTATCGAATGATGGTCCATCTGCTTCTAATTCTTGCATTTTGCTTTCTAATATTGCCTTTAATACATATTCACACATGCCTCCTTTTACAACAGTTAAACTATCTTCCTATGTTTCATCATCAATATTAGCTGCttt                                                                             <  2:347662/140‑1 (MQ=255)

                                              aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttt                                                                             <  1:410692/140‑1 (MQ=255)

                                                   aTCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGaa                                                                        >  1:51779/1‑140 (MQ=255)

                                                     cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAtt                                                                      >  1:274985/1‑140 (MQ=255)

                                                     cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAtt                                                                      >  2:407418/1‑140 (MQ=255)

                                                     cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAtt                                                                      <  1:489559/140‑1 (MQ=255)

                                                      gAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTACTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACACTATTAGCTGCTTTTTGAATTa                                                                     >  2:379025/1‑140 (MQ=255)

                                                          gatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATAGTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAGATATATTCATATGGTTCCTCTTCATTTTTAGCTGCTTTTTGAATaaaaaa                                                                 >  1:44463/1‑138 (MQ=255)

                                                               tCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCATCCTTTTACAACAGTTAACATATATTCATATGTTTCATCAACAATATTAACTGCTTTTTGAATTAAAGCAAttt                                                            >  1:302442/1‑140 (MQ=255)

                                                                ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGCTTCATCAACAATAATAGCGTCTTTTTGAATTAAAGCAATTTc                                                           <  1:244862/140‑1 (MQ=255)

                                                                     tGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAg                                                      <  2:274985/140‑1 (MQ=255)

                                                                       cTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGgcagca                                                    >  1:488382/1‑140 (MQ=255)

                                                                         ccTAATTCTCGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTAACACCGTTAAAATATATTCATCTGTTTCATCAACAATATTAGCTGCTTGTTGAATTAAAGCACTTTAGtaaacacc                                                  >  2:239522/1‑133 (MQ=255)

                                                                            aagtCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCGTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                               <  2:552518/137‑1 (MQ=255)

                                                                                     aTTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                      <  2:245845/140‑1 (MQ=255)

                                                                                          gCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAttt                                 >  1:406790/1‑140 (MQ=255)

                                                                                                 aaTATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTAc                          <  1:391854/140‑1 (MQ=255)

                                                                                                        ccTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAGTTTCGTCAGCATCTTTTTGGTCTCTTATTTTATCTActgcttta                   >  1:293097/1‑133 (MQ=255)

                                                                                                         cTTTAATTCTTGTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAg                  <  1:18008/140‑1 (MQ=255)

                                                                                                               ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGTCGTCTCTAATTTTATCTACAGTATTAGAAATGc            <  1:392423/140‑1 (MQ=255)

                                                                                                               ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc            <  1:356812/140‑1 (MQ=255)

                                                                                                               ttCTTTTTCAGTCATGCCTCCTGTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTACATCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc            <  2:280886/140‑1 (MQ=255)

                                                                                                                tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt           <  2:386979/140‑1 (MQ=255)

                                                                                                                         gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTGATTAACAGTATTTACTCAATTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGACATGCTTATTAATGa  >  2:256763/1‑140 (MQ=255)

                                                                                                                         gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGa  <  2:217178/140‑1 (MQ=255)

ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGA  >  USA300TCH1516_ALE/1646059‑1646319

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