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
A1 F16 I1 R1	9	28.1	657842	93.6%	615740	139.9

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	96.4%	71.8 / NA	28	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (13/14); minor base T (0/1); total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTT  >  USA300TCH1516_ALE/1646056‑1646311

aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGCCTCCTTTTa                                                                                                                      >  1:313960/1‑140 (MQ=255)

  cACTTGCAACACCATGTGGTAATGCACCTCTATGACCATATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTaca                                                                                                                    <  2:99403/140‑1 (MQ=255)

         aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTTCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACCACAGTTa                                                                                                             >  2:305993/1‑140 (MQ=255)

         aaCACCATGTAGTAATGCACCTCTATGACCTGATGCTACAATCGTATCGAATGATGGTCCATCTTCTCCTAATTCTAGCATTTTGCTTTCTATTATTGCCTTTAATTCTTTTTCCAAAATACCTCCTTTTACAACAGTTa                                                                                                             <  2:119598/140‑1 (MQ=255)

           cacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                           <  1:233258/140‑1 (MQ=255)

                        tGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACATTTAAAATATATTTCTATg                                                                                              >  2:169078/1‑140 (MQ=255)

                              tctATGACCAGATGCTACAATCGTATCTAATGATGGTGCAACTGCACCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcat                                                                                        <  1:60551/140‑1 (MQ=255)

                                         aTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAAAAATATTa                                                                             >  2:14818/1‑140 (MQ=255)

                                          tGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAg                                                                            <  1:127179/140‑1 (MQ=255)

                                               cAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCTTCCTTTTACAACAGTTGAAATATATTCATATGTTTGATAATCAACATTAccttct                                                                       >  2:306680/1‑140 (MQ=255)

                                                            tgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                          <  1:269385/140‑1 (MQ=255)

                                                                      tCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                <  1:188723/140‑1 (MQ=255)

                                                                           tCCTAATTCTAGCATTTTGCTTTCTAATATTTTCTTTCGGCCAACAACAAGCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                           <  1:60870/140‑1 (MQ=255)

                                                                            ccTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATc                                          >  2:237147/1‑140 (MQ=255)

                                                                             cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTAATATGTTTTATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTATTCAGCAttt                                         >  2:327160/1‑138 (MQ=255)

                                                                               aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTTCTTTTCCTGCACTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                       <  1:309237/140‑1 (MQ=255)

                                                                                 ttCTATCATTTTTCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGa                                     <  1:78344/140‑1 (MQ=255)

                                                                                   cTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTTATATGTTTCATCAACAATATTAGCTGCTTTTTTAATTAAATAAATTTTATCAGCATCTTTTAca                                   >  1:210347/1‑139 (MQ=255)

                                                                                   cTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTATAGCAATTTCGTCAGCATCTTTGACg                                   <  2:21822/140‑1 (MQ=255)

                                                                                   cTAGCATGTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCGTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACg                                   <  2:22472/140‑1 (MQ=255)

                                                                                                  cTAATATTGCCTTTAATTTTTTTTCAGTCATGCCTTCTTTTACAACAGTTAAAAGATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCt                    <  1:132326/140‑1 (MQ=255)

                                                                                                    attatTTCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACTGTTAAAATATATTCATATGTTTCATCAACTATATTAGCTGCTTTTTGAATTAATGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTAc                  <  2:82757/138‑1 (MQ=255)

                                                                                                        ttGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTATAATTTTATCTACAGTa              >  1:54125/1‑140 (MQ=255)

                                                                                                         tGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt             >  1:267755/1‑140 (MQ=255)

                                                                                                                 aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTTTCCATCATCGACGTCTCTAATTTTATCTACAGTATTAGAAATg     >  1:309167/1‑140 (MQ=255)

                                                                                                                  ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc    >  1:23955/1‑140 (MQ=255)

                                                                                                                   tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt   <  1:320120/140‑1 (MQ=255)

                                                                                                                    cTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTACAAATCCtt  >  2:228539/1‑140 (MQ=255)

ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTT  >  USA300TCH1516_ALE/1646056‑1646311

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