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 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	749,249	C→T	S59S (AGC→AGT)	setC →	Sugar efflux transporter C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	749,249	0	C	T	100.0%	131.7 / NA	40	S59S (AGC→AGT)	setC	Sugar efflux transporter C
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/22); total (18/22)

ATTATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATATT  >  USA300TCH1516_ALE/749107‑749392

aTTATAAACTCTTTGTTGCTAATATGTTGCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGtt                                                                                                                                            <  4:340637/148‑1 (MQ=255)

 ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTTTTTTTTTTTATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           >  4:412542/1‑148 (MQ=255)

 ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           <  3:112790/148‑1 (MQ=255)

 ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           <  3:139993/148‑1 (MQ=255)

   ataAACTCGTGGTTGCTAATATGTTTCTACGAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACGAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTAc                                                                                                                                         <  4:233387/148‑1 (MQ=255)

          ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  3:164586/1‑148 (MQ=255)

          ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  4:14778/1‑148 (MQ=255)

          ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  4:108554/1‑148 (MQ=255)

            ttgttgCTAATATGTTTCTACTAGGTCTGGGTATTGCCGTTACGGTCCCACATCTTGTTCATTTTGCCCCTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTc                                                                                                                                <  3:104124/148‑1 (MQ=255)

                tgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTaaa                                                                                                                                   <  1:62045/141‑1 (MQ=255)

                tgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAatt                                                                                                                            <  3:57550/148‑1 (MQ=255)

                 gCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTAAGTTTACAGGAAAt                                                                                                                                  >  2:35010/1‑141 (MQ=255)

                        tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGTATTTTAATTTTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTCCAGTAAATTCAATTATTGCTAg                                                                                                                    >  4:138288/1‑148 (MQ=255)

                        tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAg                                                                                                                    >  4:39248/1‑148 (MQ=255)

                                      aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:24145/148‑1 (MQ=255)

                                      aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      >  3:328461/1‑148 (MQ=255)

                                      aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:332829/148‑1 (MQ=255)

                                      aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:24139/148‑1 (MQ=255)

                                      aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATCACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      >  3:53903/1‑148 (MQ=255)

                                                           ccATATCTTGTTCTTTTTGCAACTAAAGATCTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAatta                                                                                 <  3:173252/148‑1 (MQ=255)

                                                                   tGTTCTTTTTGCAATTAAAGATTTAGGTATGACAACAAAGCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTTGGATTTGCATCACTTTAATAGAAAAattat                                                                                <  2:40258/141‑1 (MQ=255)

                                                                   tGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAattattattatt                                                                         <  4:147028/148‑1 (MQ=255)

                                                                    gTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtc                                                                        >  4:398832/1‑148 (MQ=255)

                                                                     ttCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtct                                                                       >  3:278130/1‑148 (MQ=255)

                                                                     ttCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtct                                                                       >  3:276069/1‑148 (MQ=255)

                                                                              cAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCg                                                                     >  2:9730/1‑141 (MQ=255)

                                                                                aCTAAAGATTTAGGTAGGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTaa                                                            >  3:365959/1‑148 (MQ=255)

                                                                                 cTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAAt                                                           <  3:167294/148‑1 (MQ=255)

                                                                                                 gACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGtttt                                           <  3:245706/148‑1 (MQ=255)

                                                                                                 gACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGtttt                                           <  4:353640/148‑1 (MQ=255)

                                                                                                            aGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGCTTTTCGGATACGCATCACTTTAATAGAAATATTATTATTATTCTCGCATTATTAGTGGGTGCGCTTGGTTTTTCAATATACtt                                <  4:194979/148‑1 (MQ=255)

                                                                                                             gTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACttt                               >  3:370671/1‑148 (MQ=255)

                                                                                                              tATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACtttt                              <  3:412542/148‑1 (MQ=255)

                                                                                                                     tACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGa                       >  3:374764/1‑148 (MQ=255)

                                                                                                                              cATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTg              <  3:414175/148‑1 (MQ=255)

                                                                                                                               aTCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTgg             >  3:128670/1‑148 (MQ=255)

                                                                                                                                tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGt            >  3:249253/1‑148 (MQ=255)

                                                                                                                                tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGt            <  3:398832/148‑1 (MQ=255)

                                                                                                                                       cGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCat     <  4:32812/148‑1 (MQ=255)

                                                                                                                                          ttAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATAtt  <  4:325470/148‑1 (MQ=255)

ATTATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATATT  >  USA300TCH1516_ALE/749107‑749392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A