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	2,272,733	C→T	intergenic (‑339/‑342)	glmS ← / → mtlA	Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]/PTS system mannitol‑specific EIICB component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,272,733	0	C	T	100.0%	107.9 / NA	31	intergenic (‑339/‑342)	glmS/mtlA	Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]/PTS system mannitol‑specific EIICB component
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (15/16); total (15/16)

CGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGCACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTGTTGTT  >  USA300TCH1516_ALE/2272602‑2272861

cGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATaa                                                                                                                         <  1:50927/141‑1 (MQ=255)

   tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAGTACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               >  4:4739/1‑148 (MQ=255)

   tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:336023/148‑1 (MQ=255)

   tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:178669/148‑1 (MQ=255)

   tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               >  4:362365/1‑148 (MQ=255)

   tCTTATTAACTTTCTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:90782/148‑1 (MQ=255)

            cTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAAc                                                                                                      >  3:88455/1‑148 (MQ=255)

                 tCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTa                                                                                                 >  4:195301/1‑148 (MQ=255)

                       aaGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTc                                                                                           <  3:77869/148‑1 (MQ=255)

                          tCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTcaaa                                                                                        <  3:129707/148‑1 (MQ=255)

                             cccTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTcaaatac                                                                                     >  3:292592/1‑148 (MQ=255)

                                     ttttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  4:259242/148‑1 (MQ=255)

                                     ttttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  3:228609/148‑1 (MQ=255)

                                     ttgtACTTAATAAGCTAGCGAATGGGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTCTCCTCCTCGTCTACAAATTCATATTTTGTACTCTATAAAGGCCACTCCTATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  4:386187/145‑1 (MQ=255)

                                      tttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattta                                                                            >  3:43820/1‑148 (MQ=255)

                                                aaGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAgg                                                                  <  3:263879/148‑1 (MQ=255)

                                                  gCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcg                                                                >  4:64785/1‑148 (MQ=255)

                                                    tAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATCTTGTACTCTATAAAGGCCACTCATCTATTAACCTTTAATCTTCACATACACATAGTCATTTGccc                                                                     >  2:14964/1‑139 (MQ=255)

                                                         aaTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcg                                                                >  2:21147/1‑141 (MQ=255)

                                                          aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcgc                                                               <  1:5667/141‑1 (MQ=255)

                                                          aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcgc                                                               <  1:5683/141‑1 (MQ=255)

                                                          aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACt                                                        >  3:294393/1‑148 (MQ=255)

                                                          aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACt                                                        <  3:10366/148‑1 (MQ=255)

                                                              gCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTAc                                                    <  4:52940/148‑1 (MQ=255)

                                                                 acaTCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  4:340426/1‑148 (MQ=255)

                                                                 acaTCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  3:163891/1‑148 (MQ=255)

                                                                        ggATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  2:3595/1‑141 (MQ=255)

                                                                                 ccgccgATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCttt                                 <  4:65887/148‑1 (MQ=255)

                                                                                           aTTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCa                       <  3:362365/148‑1 (MQ=255)

                                                                                             tCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATCAATCatt                     >  3:190154/1‑148 (MQ=255)

                                                                                                                tCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTgttgtt  >  4:280231/1‑148 (MQ=255)

CGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGCACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTGTTGTT  >  USA300TCH1516_ALE/2272602‑2272861

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A