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
A7 F1 I1 R1	776	60.0	3074904	90.1%	2770488	104.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,544,384	C→T	pseudogene (381/381 nt)	yddK ←	pseudogene, leucine‑rich protein, putative glycoportein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,544,384	0	C	T	100.0%	227.6 / NA	71	pseudogene (381/381 nt)	yddK	pseudogene, leucine‑rich protein, putative glycoportein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (39/32); total (39/32)

GGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAACTTTTAT  >  NC_000913/1544265‑1544518

gggTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTgg                                                                                                                     >  1:1520901/1‑139 (MQ=255)

           tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                          <  2:1520901/139‑1 (MQ=255)

           tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAAGAAAACGaa                                                                                                          >  2:1102662/1‑138 (MQ=255)

               cGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGt                                                                                                      >  1:352195/1‑139 (MQ=255)

                 tATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTcc                                                                                                    >  1:380397/1‑139 (MQ=255)

                   tGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAg                                                                                                  >  2:1276572/1‑139 (MQ=255)

                   tGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAg                                                                                                  >  2:1161841/1‑139 (MQ=255)

                   tGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAg                                                                                                  <  2:1526523/139‑1 (MQ=255)

                            tCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                                         >  2:1340479/1‑139 (MQ=255)

                               aCCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCgg                                                                                      >  2:104180/1‑139 (MQ=255)

                                    tCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                                 <  2:24577/139‑1 (MQ=255)

                                            tGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                                   <  1:823466/129‑1 (MQ=255)

                                            tGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                                   >  2:823466/1‑129 (MQ=255)

                                                tCTAAATGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                                     <  2:1483575/139‑1 (MQ=255)

                                                     aGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTg                                                                <  2:380397/139‑1 (MQ=255)

                                                         ttACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaat                                                            >  2:198385/1‑139 (MQ=255)

                                                           aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 <  1:1391459/100‑1 (MQ=255)

                                                           aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 >  2:1391459/1‑100 (MQ=255)

                                                           aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGAt                                                                  >  2:629543/1‑131 (MQ=255)

                                                           aCATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGAt                                                                  <  1:629543/131‑1 (MQ=255)

                                                                  aaCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                                     <  2:1219613/121‑1 (MQ=255)

                                                                  aaCTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                                     >  1:1219613/1‑121 (MQ=255)

                                                                       tattatCAACAAGACCAGACACTTATCGAATTAGTGATGTTTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGCCTATCGGTTCCTCTCTTATTGCCTGCTTGTAATAATCGTTATTACag                                              >  2:632854/1‑139 (MQ=255)

                                                                       tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 <  2:907024/88‑1 (MQ=255)

                                                                       tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 >  1:907024/1‑88 (MQ=255)

                                                                       tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCgg                                                                                      <  1:219230/99‑1 (MQ=255)

                                                                       tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCgg                                                                                      >  2:219230/1‑99 (MQ=255)

                                                                            tCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                                       <  2:390700/109‑1 (MQ=255)

                                                                            tCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGc                                                                       >  1:390700/1‑109 (MQ=255)

                                                                             caacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagta                                        <  1:1161841/139‑1 (MQ=255)

                                                                              aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATg                                                                                                                           >  1:688230/1‑55 (MQ=255)

                                                                              aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATg                                                                                                                           <  2:688230/55‑1 (MQ=255)

                                                                              aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGa                                                                   >  1:1197312/1‑111 (MQ=255)

                                                                              aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGa                                                                   <  2:1197312/111‑1 (MQ=255)

                                                                               acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagt                                         <  2:422007/136‑1 (MQ=255)

                                                                               acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagt                                         >  1:422007/1‑136 (MQ=255)

                                                                                 aaGACCAAACACTTATAGAATTAGAGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCACAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATGACAGTAAGTATTGt                                    >  1:939182/1‑139 (MQ=255)

                                                                                   gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTgga                                                                                                                    <  2:210763/57‑1 (MQ=255)

                                                                                   gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTgga                                                                                                                    >  1:210763/1‑57 (MQ=255)

                                                                                     ccAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAt                                <  2:1472674/139‑1 (MQ=255)

                                                                                      cAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                                   >  2:1016759/1‑87 (MQ=255)

                                                                                      cAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                                   <  1:1016759/87‑1 (MQ=255)

                                                                                           acTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATc                          >  2:132558/1‑139 (MQ=255)

                                                                                               ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                                 >  1:824360/1‑80 (MQ=255)

                                                                                               ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                                 <  2:824360/80‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                          >  2:1517805/1‑47 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                                          <  1:1517805/47‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 >  2:654623/1‑56 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                                 <  1:654623/56‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                                         >  1:291945/1‑64 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                                         <  2:291945/64‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTa                                                                           <  2:1000655/78‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTa                                                                           >  1:1000655/1‑78 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagta                                        >  1:502504/1‑113 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagta                                        <  2:502504/113‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAtt                               >  2:1120319/1‑122 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAtt                               <  1:1120319/122‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTc                   >  1:95582/1‑134 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTc                   <  2:95582/134‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCa                  >  1:971756/1‑135 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCa                  <  2:971756/135‑1 (MQ=255)

                                                                                                       aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt              >  1:334569/1‑139 (MQ=255)

                                                                                                       aGTGATGATTTAGTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTACAGAAGGCCTATCGGTTCCTAGCTTATTGTCTGATTGTAATAATCGTTATTACAGTAACTATTTTTTCTTTCATCTCAGGTCATGtt              >  2:934193/1‑139 (MQ=255)

                                                                                                          gatgatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTc                   >  2:1384825/1‑131 (MQ=255)

                                                                                                          gatgatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTc                   <  1:1384825/131‑1 (MQ=255)

                                                                                                             gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaa                                                             >  1:767791/1‑86 (MQ=255)

                                                                                                             gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaa                                                             <  2:767791/86‑1 (MQ=255)

                                                                                                               tttATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAACtt      <  2:334569/139‑1 (MQ=255)

                                                                                                                   ttCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                                 <  1:1137778/60‑1 (MQ=255)

                                                                                                                   ttCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAACTTTtat  >  1:721133/1‑139 (MQ=255)

                                                                                                                   ttCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTAct                                                                                 >  2:1137778/1‑60 (MQ=255)

GGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTTTTTAACTTTTAT  >  NC_000913/1544265‑1544518

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A