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 F18 I1 R1	10	38.5	883940	94.6%	836207	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	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	96.5%	78.4 / NA	29	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (12/16); total (12/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACGG  >  USA300TCH1516_ALE/1646055‑1646326

tATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTa                                                                                                                                     >  2:246681/1‑141 (MQ=255)

 aTCACTTGCAACACCATGTGGTAATGCCCCTCTATGACCAGATGCTACAATCGTATCGACTGATGGTCCATCTGCTCCTACTTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTGTTCATTCGTGcctcc‑tgatac                                                                                                                                    >  2:351474/1‑136 (MQ=255)

   cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGGCATGCCTCC‑TTTTgcaa                                                                                                                                  >  1:290272/1‑141 (MQ=255)

   cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTTTTCAGTCATGCCTCC‑TTTTacaa                                                                                                                                  <  2:390100/141‑1 (MQ=255)

                  gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATAtt                                                                                                                   >  2:131274/1‑141 (MQ=255)

                       aaTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGCTGGGCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTTCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCatat                                                                                                              >  2:128090/1‑141 (MQ=255)

                                        aGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAtt                                                                                             >  2:415794/1‑141 (MQ=255)

                                        aGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAtt                                                                                             >  2:225114/1‑141 (MQ=255)

                                             cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCATTCATGCCTCC‑TTTTACAACATTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                        >  2:221883/1‑141 (MQ=255)

                                                   tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttttt                                                                                  <  2:150904/141‑1 (MQ=255)

                                                          gAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACTTCATTTAAAATATATTCATATGTTTATTCATTATTATTATCTGCTTTTTCAAttta                                                                           >  2:174427/1‑139 (MQ=255)

                                                            atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                         <  1:131274/141‑1 (MQ=255)

                                                            atgatgGTCCATCTGCTCCCAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                         <  1:246681/141‑1 (MQ=255)

                                                                  gTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAttt                                                                   <  1:328351/141‑1 (MQ=255)

                                                                         tGCTCCTAAGTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGc                                                            <  2:40818/141‑1 (MQ=255)

                                                                              cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCtt                                                       <  2:133778/141‑1 (MQ=255)

                                                                                      aGCAGTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtct                                               <  1:10752/141‑1 (MQ=255)

                                                                                        cATTTTGCTTTTTAATATTGCTTTTAATTCTTTTTCAGTTATGTCTCC‑TTTTACAACAGTTAAGATATATGCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                             <  2:267305/141‑1 (MQ=255)

                                                                                          ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTaa                                           >  1:302595/1‑141 (MQ=255)

                                                                                            ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAtt                                         <  1:338142/141‑1 (MQ=255)

                                                                                             tGCTTTCTAATTGTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAttt                                        <  1:388718/141‑1 (MQ=255)

                                                                                                         ttGCCTTTCTATCTGGTTCAGTCTTGCCTCC‑GTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  1:99638/141‑1 (MQ=255)

                                                                                                         ttGCCTTTAATTCTTTTTCATTTATGCTTCC‑TTTTATAACAGTTAAAATATATTCATATGTTTCATCAACAAGATTAGCTGCTTTTTGCATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  2:6785/141‑1 (MQ=255)

                                                                                                         ttGCCTTTAATTCATTTTCAGTTTTG‑CTGCGTTTAAGGACTTTTAAAATATATTCATATGTTTTATCAACTATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  2:310603/141‑1 (MQ=255)

                                                                                                                tAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAAt                     <  2:15854/141‑1 (MQ=255)

                                                                                                                 aaTTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTTTCTACAGTATTAGAAATg                    >  1:376864/1‑141 (MQ=255)

                                                                                                                   ttCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt                  <  1:393926/141‑1 (MQ=255)

                                                                                                                     cTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAACTATATTCATATGTTTCCTCTACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCTTCTTTGACGTCTCTAATTTTATCTACAGTATTCGCAATGAttt                >  2:283434/1‑140 (MQ=255)

                                                                                                                      tttttCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat               >  1:240777/1‑141 (MQ=255)

                                                                                                                           cAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg          <  1:221883/141‑1 (MQ=255)

                                                                                                                               cagtcctcc‑tTTTACATCAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGatat      <  2:243563/137‑1 (MQ=255)

                                                                                                                                   cctcc‑tTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAACATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACgg  <  1:106180/141‑1 (MQ=255)

                                                                                                                                   cctcc‑tGTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACgg  <  1:232973/141‑1 (MQ=255)

TATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACGG  >  USA300TCH1516_ALE/1646055‑1646326

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