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
A23 F43 I0 R1	23	38.0	846132	95.3%	806363	140.8

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%	84.2 / NA	29	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (14/15); total (14/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646056‑1646325

aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCCTTTTGCGTACTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTac                                                                                                                                   >  1:35598/1‑141 (MQ=255)

aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTac                                                                                                                                   >  2:115619/1‑141 (MQ=255)

 tCACTTGCAACACCATGTGGTAATGCACCTCTCTGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTaca                                                                                                                                  <  1:213773/141‑1 (MQ=255)

       gCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGtt                                                                                                                            <  1:357988/141‑1 (MQ=255)

          acacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                                         >  2:391133/1‑141 (MQ=255)

           cacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaaa                                                                                                                        <  2:259516/141‑1 (MQ=255)

                    gTAATGCACCTCTTTGACCAGATGCTACAATCGTATCGAATTATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCTTGCCTCCTTTTACAACAGTTAAAATATATTCat                                                                                                               <  2:94219/141‑1 (MQ=255)

                    gTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCat                                                                                                               <  2:42287/141‑1 (MQ=255)

                         gCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTAAAACAGTTAAAATATATTCATATCtt                                                                                                          >  2:246621/1‑141 (MQ=255)

                             gtgtATGACCAGATGCTACAATCGTATCGAATGATGGTCGATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGTCTTTCATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcat                                                                                                      <  2:142268/138‑1 (MQ=255)

                                  tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCGGTCATGCCTCCTTTTACAACAGTTAAAATATCTTAATATGTTtcctacaca                                                                                                 >  1:276052/1‑134 (MQ=255)

                                           gCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTATCTAATATTGCCTTTAATTCTGTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgct                                                                                        <  2:301036/141‑1 (MQ=255)

                                            cTACAACCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                       >  2:53370/1‑141 (MQ=255)

                                                 aTCCTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                                  <  2:383546/141‑1 (MQ=255)

                                                          aaTGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCCGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGATGATCTTTGAATTaaa                                                                         >  2:305115/1‑141 (MQ=255)

                                                                       cTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACACTATTAGCTGCTTTTTGCATTAAAGCAATTTCGTCAg                                                            >  2:148166/1‑141 (MQ=255)

                                                                                 ttCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                                  >  2:91683/1‑141 (MQ=255)

                                                                                  tCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCATCTATATTATCTGCTTTTTTAATTAAAGCAATTTCGTCAGCATCTTTTACg                                                 >  2:24448/1‑141 (MQ=255)

                                                                                       cATTTCGCTTTCTAAGATTGTCTTTCATCCGGTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                            <  1:177860/141‑1 (MQ=255)

                                                                                              cTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTa                                     <  1:53370/141‑1 (MQ=255)

                                                                                                   tAATACTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTAc                                <  1:68908/141‑1 (MQ=255)

                                                                                                        ttGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                           <  1:269393/141‑1 (MQ=255)

                                                                                                             tttAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATCTATTTGGAAGCCAGTGGTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGaa                      <  1:418560/141‑1 (MQ=255)

                                                                                                                 aTTTTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTCTCTCCAGTATTAGAAATGc                  <  2:370153/141‑1 (MQ=255)

                                                                                                                     tttttCAGGCATGCCTCCTTTTACAACAGTTAACATATATTCATATGTTTAATCAACCATATTAACTGCTTTTTGAATTAAAGCAATTTAGTTAGCATCTTTGACCTCTCTAACTTTATCTTCAGTATTAGACATGCttat              >  2:24461/1‑141 (MQ=255)

                                                                                                                      ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttatt             >  2:287035/1‑141 (MQ=255)

                                                                                                                         tCAGTCATGCCCCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGACTTAAAGCAATTTCGTCAGCATCTTTGACATCTCTAATTTTATCTTCAGTATTAGAAATGCTTATTAAt          >  1:205160/1‑141 (MQ=255)

                                                                                                                              cATTCCTCCTTTTACAACAGTTACAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTGTGAATGAAATCAATTTCGTCAGCATCTTTAGCGTCTCTAATTTTATCTACATTTTTATAAATGCTTATTAATGatat     >  2:209314/1‑141 (MQ=255)

                                                                                                                                 gCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACg  <  1:391133/141‑1 (MQ=255)

ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646056‑1646325

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