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 F43 I0 R1	23	38.0	846132	95.3%	806363	140.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	100%	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	100.0%	158.4 / ‑6.5	54	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (24/29); minor base T (1/0); total (25/29)
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.

TTGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCT  >  USA300TCH1516_ALE/2279568‑2279839

ttGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtg                                                                                                                                     >  2:185409/1‑141 (MQ=255)

ttGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtg                                                                                                                                     <  2:6280/141‑1 (MQ=255)

 tgggCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTTTTATTAGCTTGCGGTTTATCCTTTGCACCATCAGTTGCTGATGTTTCtct                                                                                                                                    >  2:413992/4‑139 (MQ=255)

                     cTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCAt                                                                                                                >  2:185651/1‑141 (MQ=255)

                        cTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCAc                                                                                                             >  1:184522/1‑141 (MQ=255)

                             ggTTTACTAGTTACATCTTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACtatta                                                                                                        <  1:194764/141‑1 (MQ=255)

                               tttACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTattatt                                                                                                      <  1:319494/141‑1 (MQ=255)

                               tttACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTattatt                                                                                                      <  2:213158/141‑1 (MQ=255)

                                      gTTACATCGTTATGCGTTGTGGGACTGTATGTTAAGGTTGCTACACTAGGATTGTTGTTGGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgtt                                                                                               <  2:407020/141‑1 (MQ=255)

                                        tACATCGTGATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgttgt                                                                                             <  1:64750/141‑1 (MQ=255)

                                           aTCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg                                                                                          <  1:20010/141‑1 (MQ=255)

                                            tCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTCTTTGGTGTTGTCGga                                                                                         >  1:343883/1‑141 (MQ=255)

                                             cGTTATCCATTGTTGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTAATCTGTTGCCGCATCACTATTATTTGGTGTTGTCGgag                                                                                        >  2:310185/1‑141 (MQ=255)

                                             cGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGgag                                                                                        >  1:149067/1‑141 (MQ=255)

                                                   ccATTGGCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGt                                                                                  <  2:305404/141‑1 (MQ=255)

                                                           ggACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTg                                                                          <  1:50653/141‑1 (MQ=255)

                                                           ggACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTg                                                                          <  1:258823/141‑1 (MQ=255)

                                                           ggACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATAACCATTAGGTGTTGTTGTCGGAGAAGCGTCTGCTTTg                                                                          >  2:68296/1‑141 (MQ=255)

                                                           ggACTGTTGTTGGATGCATCTAAACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTg                                                                          <  2:631/141‑1 (MQ=255)

                                                             aCTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTTCCGCGTCACTATTTTTTGGTGTTGTCGGCGACGCGTCTGCTTTAcc                                                                        >  1:178974/1‑141 (MQ=255)

                                                             aCTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGcc                                                                        <  1:281355/141‑1 (MQ=255)

                                                              ttgtttgttGTTTCATTTTCTCTTGAATTTTTATTAGCTTTCTGTTTATCATTTGTATCATCAGTTGTTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTTGTGTTGTCGGAGATGCGTCTGCTTTGCCa                                                                       <  2:371503/140‑1 (MQ=255)

                                                                 tttgttGGTGCATTTATACTAGATTTGTTATTATCTTGCGGTTTATCATTTGCATCATCTGTTGCTGATCTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTa                                                                    <  2:423034/141‑1 (MQ=255)

                                                                  ttgttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGCAGCGTCTGCTTTTCCATTat                                                                   >  2:298170/1‑140 (MQ=255)

                                                                   tgttgATGCATCTACACTAGAATTGTTAGTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc                                                                  <  1:210839/141‑1 (MQ=255)

                                                                    gttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCTGCATCACTATTAGTTGGTGTTGTCCGATAAGCGTCTGCTTTGCCTTTAGCt                                                                 >  2:223705/1‑141 (MQ=255)

                                                                          gCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcgtc                                                           >  1:256663/1‑141 (MQ=255)

                                                                              cTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAg                                                       <  1:393952/141‑1 (MQ=255)

                                                                               tACACTAGAATTGTTATTATCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGa                                                      <  1:293465/141‑1 (MQ=255)

                                                                                 cacTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCGTTAGCTGTCGTCTCAGAtg                                                    >  1:290901/1‑140 (MQ=255)

                                                                                     aGATTTGTTATTAGCTTTCGGTTTTTCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGtt                                                <  2:138944/141‑1 (MQ=255)

                                                                                     aGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATCAGCTGCCGTCTCAGATACGtt                                                >  1:2974/1‑141 (MQ=255)

                                                                                     aGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCAGTAGCTGTCGTCTCAGATACGtt                                                >  1:96995/1‑141 (MQ=255)

                                                                                         ttGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCGTCACTATGATTTGGTGTTGTCTGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGt                                            <  1:310883/141‑1 (MQ=255)

                                                                                           gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTg                                          >  1:99051/1‑141 (MQ=255)

                                                                                           gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTATTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGCTACGGTATGTTg                                          >  2:277055/1‑141 (MQ=255)

                                                                                           gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGACGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAACTGCTCTCTCAGATACGTCAGGTTg                                          >  2:378692/1‑141 (MQ=255)

                                                                                                ttgCTGGCGGTTGATCCTTTGCATCATTGGTTGCTGATGTTACTGTTGTGTCACCTGGTGCCGCATCGCTTTTAGTTGGTGTTGGTGGAGAAGCGTCTGCTTTGCTGTGAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg                                     <  2:173162/139‑1 (MQ=255)

                                                                                                taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg                                     <  1:185409/141‑1 (MQ=255)

                                                                                                taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCCCAGATGCGTTATTTTGTCCAg                                     <  2:370163/141‑1 (MQ=255)

                                                                                                 aGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGt                                    >  2:231998/1‑141 (MQ=255)

                                                                                                  gCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTa                                   >  1:365260/1‑141 (MQ=255)

                                                                                                         gTTTATCATTTGCATCAGCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg                            <  1:121712/141‑1 (MQ=255)

                                                                                                          tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTgg                           <  2:219269/141‑1 (MQ=255)

                                                                                                               cATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTg                      <  1:376638/141‑1 (MQ=255)

                                                                                                                   tGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAtt                  >  1:333796/1‑141 (MQ=255)

                                                                                                                       tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCCTCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCa              <  1:172099/141‑1 (MQ=255)

                                                                                                                       tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTGGGTTGTCCAGTATTTTCTGGTGTTGCATTGGcc              >  1:108981/1‑140 (MQ=255)

                                                                                                                         atcaGTTGCTGATGTTACTGTTGTTTCACCTGTGGCCACATCACTATTATTTGGTGTTGTCGGAGCAGCGTCTGCTTTGCCATTAGCTGTAGTCTCAGATACGTTAGGTTGTCCAGTCTTTTCTGGTGTTGCATTAGTAtt            >  2:18090/1‑141 (MQ=255)

                                                                                                                         atcaGTTGCTGAGGGTACTGTTGTTTCACCTGTTGCTGCATCACTCTTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTCCCATTAGCTGTCGTCTTAGATACGTTGTGTTCTCACATATTTTCTAGCGTTGGATTACCAtt            >  2:19187/1‑141 (MQ=255)

                                                                                                                            aGTTGCTGATGTTACTGTTGTTTCACCTGTTTCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCTATTATCTGTCGTCTCATATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGa         <  2:258125/141‑1 (MQ=255)

                                                                                                                              ttGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAt       <  1:44085/141‑1 (MQ=255)

                                                                                                                                  tGATGGTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGGTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGc   <  1:348962/141‑1 (MQ=255)

                                                                                                                                   gATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTATTGTGTCGCATTAGCATTTAATTTTGCt  >  2:238645/1‑141 (MQ=255)

TTGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCT  >  USA300TCH1516_ALE/2279568‑2279839

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