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 F68 I0 R1	25	50.4	1217238	93.3%	1135683	133.9

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%	134.9 / ‑6.5	46	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (14/31); minor base T (0/1); total (14/32)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAAT  >  USA300TCH1516_ALE/1646060‑1646317

cTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTATAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCttt                                                                                                                              <  2:352845/134‑1 (MQ=255)

     aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                         <  1:552642/134‑1 (MQ=255)

     aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                         <  2:457735/134‑1 (MQ=255)

            tgtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACACTTaa                                                                                                                  >  2:373781/1‑134 (MQ=255)

                     gCACCTCTATGACCAGATGCTACCATCGTATCGAATGATGGTCCCTCTGCTCCTAAGTCGAGCATTCTGCTGTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTc                                                                                                         <  1:187309/134‑1 (MQ=255)

                      cACCTCTACTACGCGATGCTACAATCGTATCGGCTGATGGTCCATCTGCGCCTAATTCTAGCACTTTGCTTTCTAATATTGCATTTAATTCTTTTTCAGTCATGCCTCATTTTATAACAGTTAAAATATATTCa                                                                                                        <  2:475089/134‑1 (MQ=255)

                          tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                    <  2:443151/134‑1 (MQ=255)

                          tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCAGCTGCTCCTAATTCTAGCATTTTGCTTTCTCATACTGCATTTAATTCTTTTTCAGTCATTCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                    <  2:8957/134‑1 (MQ=255)

                          tcgaTGACCAGCTCCTCCACTCGTATCGAATGATGGTCCATCTCCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                    <  2:451591/131‑1 (MQ=255)

                                aCCAGATGCTACAATCGTATCTAATGATGGTCCATCTGCTTCTAATTCTAGCATTTTGCTTTCTAATATTCCCTTTTTTTTTTTTGCAAACATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcat                                                                                              <  2:128747/134‑1 (MQ=255)

                                aCCAGATGCTACAATCGTATCGAATGATGTTCCATCTGCTCCCAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATACTCATATATTtcac                                                                                              >  2:248270/1‑133 (MQ=255)

                                     aTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATAGTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATcaaca                                                                                         <  1:70747/134‑1 (MQ=255)

                                            aaTTGTATCGATTGGTGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAg                                                                                  <  2:12538/134‑1 (MQ=255)

                                            aaTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAg                                                                                  <  1:328177/134‑1 (MQ=255)

                                                gTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGATTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATCTTTCATCAATAATATTAgctgc                                                                              >  2:201354/1‑134 (MQ=255)

                                                  aTCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtt                                                                            >  2:336966/1‑134 (MQ=255)

                                                   tCGAATGATGGTCCTTCTCCTCCTTATTCTAGCTTTTTGCCTGGTTATATTGCCGTTAAGTCTTTTTCAGTCATGCCTCCGTTTACAACAGTTAAAATATATTCATATGGTTCATCAACAATATTAGCTGCttt                                                                           <  1:113256/134‑1 (MQ=255)

                                                       atgatgGTGCATCTGCTCCTAATTCTAGCATTTTGCCTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTTGCTGCTTTTTGa                                                                       <  2:466822/134‑1 (MQ=255)

                                                       atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGa                                                                       <  1:339517/134‑1 (MQ=255)

                                                           tgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTa                                                                   <  1:596393/134‑1 (MQ=255)

                                                                cATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAAAAATATTAGCTGCTTTTTGAATTAAAACa                                                              >  2:7051/1‑134 (MQ=255)

                                                                     gCTCCTAATTCTAGCATTTTGCTGTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCATTTTACAACAGTTAAAATATATTAATATGTTTCATCGACAATATTAGCTACTATTTGAATTAAAGCAATTTc                                                         >  2:319738/1‑134 (MQ=255)

                                                                       tCCTAATTCTCGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATGTTAGCTGCTTTTTGAATTAAAGCAATTTCGt                                                       <  2:249401/134‑1 (MQ=255)

                                                                         cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCACCAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCa                                                     >  1:594245/1‑134 (MQ=255)

                                                                           aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGc                                                   <  1:327080/134‑1 (MQ=255)

                                                                             ttCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                                 <  1:544792/134‑1 (MQ=255)

                                                                              tCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTCGAATTAAAGCAATTTCGTCAGCATc                                                <  1:578012/134‑1 (MQ=255)

                                                                                 aGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                             <  2:232642/134‑1 (MQ=255)

                                                                                  gCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCCTCAACAATATTAGCTGCTTTTTGAATTAAAACAATTTCGTCAGCATCTTTg                                            >  1:501965/1‑134 (MQ=255)

                                                                                    aTTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                          <  1:133382/134‑1 (MQ=255)

                                                                                     ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACg                                         <  2:365633/134‑1 (MQ=255)

                                                                                       ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtc                                       <  1:336966/134‑1 (MQ=255)

                                                                                          cTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTCTGAATTAAAGCAATTTCGTCAGCATCTTTGTCGTctct                                    >  1:200998/1‑134 (MQ=255)

                                                                                                   atttgcTTTTATTCTTTTTCTGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATc                           <  2:450855/129‑1 (MQ=255)

                                                                                                      gCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTAc                        <  2:14536/134‑1 (MQ=255)

                                                                                                        cTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAg                      <  1:555593/134‑1 (MQ=255)

                                                                                                             aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCGCTAATTTTATCTACATAATTa                 >  2:373840/1‑134 (MQ=255)

                                                                                                                   tttCAGTCATGCCTCCTTTTACCCCATTTTAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg           <  2:291355/134‑1 (MQ=255)

                                                                                                                   tttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg           >  2:326639/1‑134 (MQ=255)

                                                                                                                   tttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg           <  1:545909/134‑1 (MQ=255)

                                                                                                                   tttCAGCCATGCCTCCTTTTACAGCATTTAAAATATATTCATATGTTTCATCAACAATATTCGCTGCTTTTTGTATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg           <  2:295403/134‑1 (MQ=255)

                                                                                                                       aGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTCTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta       >  1:372365/1‑134 (MQ=255)

                                                                                                                        gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat      <  1:386755/134‑1 (MQ=255)

                                                                                                                          cATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGACATGCtcatta    >  2:454002/1‑134 (MQ=255)

                                                                                                                            tGCCTTCTTTTATTATATTTAAAATACATTCATATGTCTCATCAACAATACTAGCTGCTTTTTGGACTAGAGCAATCTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAAt  <  1:55828/134‑1 (MQ=255)

                                                                                                                            tGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAAt  >  2:131595/1‑134 (MQ=255)

CTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAAT  >  USA300TCH1516_ALE/1646060‑1646317

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A