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
A10 F28 I1 R1	126	51.4	1736588	99.0%	1719222	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,419,175	A→G	pseudogene (134/1025 nt)	yhdW →	putative ABC transporter periplasmic binding protein YhdW

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,419,175	0	A	G	100.0%	196.6 / NA	56	pseudogene (134/1025 nt)	yhdW	putative ABC transporter periplasmic binding protein YhdW
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (27/29); total (27/29)

ATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTACCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCTCACTGCAAAAGAACGCTT  >  NC_000913/3419039‑3419309

aTTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCt                                                                                                                                     <  1:828785/140‑1 (MQ=255)

aTTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCt                                                                                                                                     <  2:45420/140‑1 (MQ=255)

aTTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCt                                                                                                                                     <  1:324651/140‑1 (MQ=255)

 ttATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTg                                                                                                                                    >  1:167657/1‑140 (MQ=255)

  tATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTgg                                                                                                                                   >  1:161974/1‑140 (MQ=255)

   aTGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTggg                                                                                                                                  >  1:406947/1‑140 (MQ=255)

   aTGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTggg                                                                                                                                  <  2:825823/140‑1 (MQ=255)

   aTGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTggg                                                                                                                                  >  1:392903/1‑140 (MQ=255)

   aTGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTggg                                                                                                                                  <  2:167657/140‑1 (MQ=255)

   aTGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTggg                                                                                                                                  <  2:405482/140‑1 (MQ=255)

         aaGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTctct                                                                                                                            >  1:232499/1‑140 (MQ=255)

         aaGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTctct                                                                                                                            >  2:458315/1‑140 (MQ=255)

                tgatAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCg                                                                                                                     >  1:507110/1‑140 (MQ=255)

                     gCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCt                                                                                                                <  1:506782/140‑1 (MQ=255)

                     gCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCt                                                                                                                <  2:830126/140‑1 (MQ=255)

                         cacTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACg                                                                                                            >  2:645246/1‑140 (MQ=255)

                          acTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACgg                                                                                                           >  2:32161/1‑140 (MQ=255)

                              gCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAg                                                                                                       >  1:703344/1‑140 (MQ=255)

                              gCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAg                                                                                                       >  1:206503/1‑140 (MQ=255)

                              gCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAg                                                                                                       >  2:91211/1‑140 (MQ=255)

                                tGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGtt                                                                                                     <  1:458315/140‑1 (MQ=255)

                                 gccgccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGttt                                                                                                    >  1:309013/1‑140 (MQ=255)

                                 gccgccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGttt                                                                                                    <  2:61905/140‑1 (MQ=255)

                                   cgccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTc                                                                                                  <  2:392903/140‑1 (MQ=255)

                                   cgccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTc                                                                                                  <  1:834331/140‑1 (MQ=255)

                                    gccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTc                                                                                                  <  2:536947/139‑1 (MQ=255)

                                    gccAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTc                                                                                                  >  1:536947/1‑139 (MQ=255)

                                         cGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTAt                                                                                            <  1:645246/140‑1 (MQ=255)

                                         cGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTAt                                                                                            <  2:749452/140‑1 (MQ=255)

                                           tgctgcTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTg                                                                                          <  2:507110/140‑1 (MQ=255)

                                            gctgctTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGa                                                                                         >  2:201834/1‑140 (MQ=255)

                                                  tGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGa                                                                                   >  2:391886/1‑140 (MQ=255)

                                                     cGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGatat                                                                                <  2:309013/140‑1 (MQ=255)

                                                                 ggCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGgtgt                                                                    <  2:493835/140‑1 (MQ=255)

                                                                  gcgcTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGtt                                                                   >  2:612177/1‑140 (MQ=255)

                                                                      tgctgGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCg                                                               <  2:406947/140‑1 (MQ=255)

                                                                      tgctgGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCg                                                               <  1:201834/140‑1 (MQ=255)

                                                                      tgctgGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCg                                                               <  2:703344/140‑1 (MQ=255)

                                                                      tgctgGCGCGACGCTTGATGCCATTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCg                                                               <  1:612177/140‑1 (MQ=255)

                                                                        ctgGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCgct                                                             >  1:221907/1‑140 (MQ=255)

                                                                        ctgGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCgct                                                             <  2:206503/140‑1 (MQ=255)

                                                                          ggCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCgctgc                                                           <  1:265538/140‑1 (MQ=255)

                                                                              cgACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTa                                                       <  1:391886/140‑1 (MQ=255)

                                                                                aCGCTTGATGTCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTAtt                                                     >  2:355558/1‑140 (MQ=255)

                                                                                aCGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTAtt                                                     >  2:40268/1‑140 (MQ=255)

                                                                                      gATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTga                                               <  1:91211/140‑1 (MQ=255)

                                                                                             ttCAGAAAAAAGGTTTTGTGCAATGCGGGGTCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGCAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACg                                        >  2:475225/1‑140 (MQ=255)

                                                                                                  aaaaaaGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGt                                   >  1:546797/1‑140 (MQ=255)

                                                                                                  aaaaaaGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGt                                   >  2:479592/1‑140 (MQ=255)

                                                                                                       aGGTTTTGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAat                              >  1:754796/1‑140 (MQ=255)

                                                                                                            ttGTGCAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATAcc                         >  1:570806/1‑140 (MQ=255)

                                                                                                                 cAATGCGGGATCAGTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCt                    <  1:355558/140‑1 (MQ=255)

                                                                                                                              gTGATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCTCACTGCAAAAGaa       <  1:32161/140‑1 (MQ=255)

                                                                                                                                gATGGATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCTCACTGCAAAAGAACg     >  1:250718/1‑140 (MQ=255)

                                                                                                                                   ggATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCt                    <  2:164475/122‑1 (MQ=255)

                                                                                                                                   ggATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCt                    >  1:164475/1‑122 (MQ=255)

                                                                                                                                   ggATTGCCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCTCACTGCAAAAGAACGCtt  >  1:316686/1‑140 (MQ=255)

ATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAAAGGTTTTGTGCAATGCGGGATCAGTGATGGATTACCTGGGTTCTCTTATGCCGATGCTGACGGTAAGTTTTCAGGTATTGATGTTGATATTTGTCGTGGTGTTGCCGCTGCTGTATTTGGTGACGACACGAAAGTGAAATATACCCCGCTCACTGCAAAAGAACGCTT  >  NC_000913/3419039‑3419309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A