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 F43 I0 R1	32	68.2	1528488	95.6%	1461234	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%	131.4 / ‑6.5	42	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (21/20); minor base A (1/0); total (22/20)
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.

ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGAT  >  USA300TCH1516_ALE/1646059‑1646320

aCTTGCAACACCATGTGGTAATGCACCTCTATGACTAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTTAGTAATGCCTCCTTGTacaa                                                                                                                             >  1:445364/1‑140 (MQ=255)

aCTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTAACATCGAATCGAATGATGATCCATCGGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCATTCATTCCTCCTTTTacaa                                                                                                                             >  1:178028/1‑140 (MQ=255)

     cAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGtt                                                                                                                        >  2:322609/1‑140 (MQ=255)

        cacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                                     <  2:36929/140‑1 (MQ=255)

             tgtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAACatata                                                                                                                >  2:137820/1‑140 (MQ=255)

              gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                                                                               <  1:514394/140‑1 (MQ=255)

              gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                                                                               >  1:49613/1‑140 (MQ=255)

                     tGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                        <  1:502401/140‑1 (MQ=255)

                     tGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                        <  1:442691/140‑1 (MQ=255)

                          ctctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtca                                                                                                   >  2:295423/1‑140 (MQ=255)

                                    aGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAatat                                                                                         <  2:749426/140‑1 (MQ=255)

                                         cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgct                                                                                    >  1:581700/1‑140 (MQ=255)

                                            cAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgct                                                                                 <  2:46992/140‑1 (MQ=255)

                                               gcGTATCGAATGATGGTCCATCTGCTCCTACTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                              <  1:284473/139‑1 (MQ=255)

                                                 gTATCAAATGATGATACATCTGCTCCTAATTCTAGCATTTTACTATCTAATATTACCTATAATTATTTTTAAATCATGCATACTTTTACAAAAGTTAAAATATATTCATATATTTAATCAATAATATTAACTAATTTTTg                                                                            >  2:223587/1‑140 (MQ=255)

                                                     cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTACAATATATTCATATGTTTCATCAACCATCTTAGCTGCTTTTTGAAtt                                                                        >  1:307781/1‑140 (MQ=255)

                                                     cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAtt                                                                        >  2:204940/1‑140 (MQ=255)

                                                        atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTaaa                                                                     <  1:236236/140‑1 (MQ=255)

                                                         cgatgGTTCGTCTGCTCCTCATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                    <  1:671386/139‑1 (MQ=255)

                                                                ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTc                                                             >  1:160906/1‑140 (MQ=255)

                                                                ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTc                                                             >  1:554009/1‑140 (MQ=255)

                                                                  aTCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCCTTTTTAATTAAAGCAATTTCGt                                                           >  2:679781/1‑140 (MQ=255)

                                                                   tCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTCCACGAGGTAAAATATATTTATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                          >  1:757755/1‑140 (MQ=255)

                                                                      gCTCCTACTTCTAGCATTTTGGTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTGTTACAACAGTTAAGATATATTCATATGTTTCATCAACAATATGAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGc                                                       <  2:713683/140‑1 (MQ=255)

                                                                               tCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGAc                                             >  1:621180/1‑140 (MQ=255)

                                                                               tCTAGCATTGTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTCTACAACCGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGAc                                             <  1:679603/140‑1 (MQ=255)

                                                                                  aGCATTGTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGtc                                          <  2:685621/140‑1 (MQ=255)

                                                                                        ttGCTTTCTAATATTGCCTTTAATTCTTTTTCTGTCATGCCTCCTTATCCATTATTTATACTATACTATTTTGTTTCATAAATTATATTAGCTGCTTTTTGAATTATAGCTGCTTGTTCATCAT‑CTTTTACGTCTCTAAt                                    <  2:377480/140‑1 (MQ=255)

                                                                                        ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAAt                                    <  1:601190/140‑1 (MQ=255)

                                                                                         tGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCACTTTCGTCAGCAT‑CTTTGACGTCTGTAAtt                                   >  2:390043/1‑140 (MQ=255)

                                                                                          gCTTTCTAATATTGCCTTTAATTCTTTTTCTGTCTTGTTTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTATCTTCTTTTTGATTTTAATCAATTTTGTCATCAT‑TTTTTACGTCTCTAtttt                                  >  2:410732/1‑140 (MQ=255)

                                                                                               cTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCt                             >  1:293303/1‑140 (MQ=255)

                                                                                                      tGCCTTTAATTCTTTTTCAGTCATGCCTCCTTGTACAACAGTTAAACTATATTCTTATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTAt                      <  1:104828/140‑1 (MQ=255)

                                                                                                        ccTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTa                    <  1:204940/140‑1 (MQ=255)

                                                                                                        ccTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTa                    <  1:306341/140‑1 (MQ=255)

                                                                                                              aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAGGCAATTTCGTGAGCAT‑GTTTGAGGACTGTGATTTTATCTAAGGTAGTAGAAATg              >  1:378987/1‑140 (MQ=255)

                                                                                                              aTTCTTTTTCAGCCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg              <  1:318942/140‑1 (MQ=255)

                                                                                                                  tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta          >  1:158753/1‑140 (MQ=255)

                                                                                                                  tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta          >  2:101427/1‑140 (MQ=255)

                                                                                                                  tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATCTTATCTACAGTATTAGAAATGCtta          <  1:295423/140‑1 (MQ=255)

                                                                                                                          tCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATTGACAATATTAGCTGCTTTTTGAATTAAATCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat  <  2:337706/140‑1 (MQ=255)

                                                                                                                          tCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGATTCATCTACAATATTAGCTGCTTTTTGACCTAACTCTATTTCGTCA‑CATGAGATAATGTCTCTAATTTTATCTACAGTATTAGAGATGCTTATTAATGat  >  1:678976/1‑140 (MQ=255)

ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAT‑CTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGAT  >  USA300TCH1516_ALE/1646059‑1646320

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