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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,251,860	(T)_7→6	pseudogene (900/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,251,854	0	T	.	100.0%	289.6 / NA	65	pseudogene (894/1323 nt)	yjbI	pseudogene, SopA‑related, pentapeptide repeats‑containing
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (28/37); total (28/37)

TCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAATTTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCTAT  >  NC_000913/4251720‑4251964

tCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttt                                                                                                            >  2:159208/1‑139 (MQ=255)

tCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttt                                                                                                            >  1:58811/1‑139 (MQ=255)

    atgaAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAAttttttatc                                                                                                        >  2:407653/1‑136 (MQ=255)

      gaAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCa                                                                                                     <  2:58811/139‑1 (MQ=255)

           tAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  2:340392/139‑1 (MQ=255)

           tAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  1:69753/139‑1 (MQ=255)

            aaCAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTAt                                                                                               >  2:540848/1‑139 (MQ=255)

              cAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCg                                                                                             >  2:134380/1‑139 (MQ=255)

                aGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  1:407653/139‑1 (MQ=255)

                 gTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATc                                                                                          <  2:543602/139‑1 (MQ=255)

                  ttCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCa                                                                                         <  1:159208/139‑1 (MQ=255)

                   tCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAg                                                                                        >  2:69987/1‑139 (MQ=255)

                    cGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAgg                                                                                       >  1:377333/1‑139 (MQ=255)

                     gatgatTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGc                                                                                      >  1:145487/1‑139 (MQ=255)

                      atgatTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     >  2:156778/1‑139 (MQ=255)

                         atTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  <  1:69987/139‑1 (MQ=255)

                              aTGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATc                                                                             <  2:23349/139‑1 (MQ=255)

                                   tCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  2:540931/139‑1 (MQ=255)

                                     aaCATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           >  2:212499/1‑118 (MQ=255)

                                     aaCATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  1:212499/118‑1 (MQ=255)

                                            aTTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGatgatatga                                                               >  1:27600/1‑139 (MQ=255)

                                             ttCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGatgatatgat                                                              <  2:27600/139‑1 (MQ=255)

                                                aGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCaa                                                           <  1:237208/139‑1 (MQ=255)

                                                            ttCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTg                                               >  1:263127/1‑139 (MQ=255)

                                                            ttCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTg                                               >  2:20931/1‑139 (MQ=255)

                                                             tCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:134380/139‑1 (MQ=255)

                                                             tCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:156778/139‑1 (MQ=255)

                                                              cGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        >  2:200370/1‑112 (MQ=255)

                                                              cGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  1:200370/112‑1 (MQ=255)

                                                               gATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  1:501255/139‑1 (MQ=255)

                                                               gATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  1:20931/139‑1 (MQ=255)

                                                                aTACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGAt                                                                              >  1:389475/1‑104 (MQ=255)

                                                                aTACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGAt                                                                              <  2:389475/104‑1 (MQ=255)

                                                                      aaCAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                >  1:31151/1‑80 (MQ=255)

                                                                      aaCAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTa                                                                                                <  2:31151/80‑1 (MQ=255)

                                                                        cAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           <  2:184192/83‑1 (MQ=255)

                                                                        cAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGAt                                                                                           >  1:184192/1‑83 (MQ=255)

                                                                         aGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATaaa                                  <  2:27705/139‑1 (MQ=255)

                                                                           atgatCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAaga                                >  1:499170/1‑139 (MQ=255)

                                                                            tgatCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  1:12867/139‑1 (MQ=255)

                                                                              atCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        >  2:121367/1‑96 (MQ=255)

                                                                              atCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACgg                                                                        <  1:121367/96‑1 (MQ=255)

                                                                                       attaACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGTATCTTTATATAGAGTGGATTCGTAg                    <  1:439632/139‑1 (MQ=255)

                                                                                           aCAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGtgat                <  2:145487/139‑1 (MQ=255)

                                                                                           aCAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGtgat                <  2:377333/139‑1 (MQ=255)

                                                                                             aGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              >  1:80413/1‑107 (MQ=255)

                                                                                             aGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  2:80413/107‑1 (MQ=255)

                                                                                              gATTTAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTgatgat             >  1:96661/1‑139 (MQ=255)

                                                                                                 ttAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  >  1:83134/1‑67 (MQ=255)

                                                                                                 ttAATACGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTa                                                                                  <  2:83134/67‑1 (MQ=255)

                                                                                                      aCGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCAcc     <  2:96661/139‑1 (MQ=255)

                                                                                                       cGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:168306/99‑1 (MQ=255)

                                                                                                       cGAATAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:168306/1‑99 (MQ=255)

                                                                                                         aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:628419/1‑97 (MQ=255)

                                                                                                         aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:421889/97‑1 (MQ=255)

                                                                                                         aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            >  1:421889/1‑97 (MQ=255)

                                                                                                         aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCa                                            <  2:628419/97‑1 (MQ=255)

                                                                                                         aaTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCtat  >  1:162374/1‑139 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     >  1:122123/1‑55 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGcc                                                                                     <  2:122123/55‑1 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGc                                                        >  2:522801/1‑84 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGc                                                        <  1:522801/84‑1 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               >  1:122059/1‑109 (MQ=255)

                                                                                                          aTAAATGGCTAATTGATAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  2:122059/109‑1 (MQ=255)

                                                                                                                          tAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              <  1:283656/78‑1 (MQ=255)

                                                                                                                          tAAAAATAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTgg                                              >  2:283656/1‑78 (MQ=255)

                                                                                                                           aaaaaTAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               >  1:333895/1‑92 (MQ=255)

                                                                                                                           aaaaaTAACAA‑TTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAagag                               <  2:333895/92‑1 (MQ=255)

TCTGATGAAGATAACAAGTTCGATGATTTTATGCGTCAACATCGATTCAGTGAGGTGAATTTCGATACCCAACAGATGATCGATTTTATTAACAGATTTAATACGAATAAATGGCTAATTGATAAAAATAACAATTTTTTTATCCAACTTATCGATCAGGCCTTACGATCAACGGATGATATGATCAAAGCAAATGTTTGGCATCTTTATAAAGAGTGGATTCGTAGTGATGATGTTTCACCTAT  >  NC_000913/4251720‑4251964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A