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 F28 I1 R1	172	67.8	2301510	98.9%	2276193	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,280,758	C→T	pseudogene (58/402 nt)	agaW →	N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,280,758	0	C	T	100.0%	187.1 / NA	53	pseudogene (58/402 nt)	agaW	N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (25/28); total (25/28)

CGCTGGGGTGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGGTGTGGATGGGGCTGG  >  NC_000913/3280621‑3280890

cGCTGGGGTGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTg                                                                                                                                    >  2:851777/1‑140 (MQ=255)

          gAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTa                                                                                                                          <  1:971317/140‑1 (MQ=255)

           aaTGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTaa                                                                                                                         <  2:337883/140‑1 (MQ=255)

           aaTGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTaa                                                                                                                         <  2:458394/140‑1 (MQ=255)

               cTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGc                                                                                                                     <  1:122587/140‑1 (MQ=255)

               cTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGc                                                                                                                     <  1:20024/140‑1 (MQ=255)

               cTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGc                                                                                                                     >  2:20024/1‑140 (MQ=255)

               cTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGc                                                                                                                     <  2:813193/140‑1 (MQ=255)

                 tCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCt                                                                                                                   <  2:22889/140‑1 (MQ=255)

                 tCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCt                                                                                                                   <  1:319590/140‑1 (MQ=255)

                 tCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCt                                                                                                                   <  1:865687/140‑1 (MQ=255)

                       aGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCa                                                                                                             <  1:1072457/140‑1 (MQ=255)

                                      agCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCggt                                                                                              <  1:133087/140‑1 (MQ=255)

                                        ccTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCatat                                                                                                          <  1:263592/126‑1 (MQ=255)

                                        ccTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCatat                                                                                                          >  2:263592/1‑126 (MQ=255)

                                        ccTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCggtgg                                                                                            >  2:128739/1‑140 (MQ=255)

                                              gtgGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCg                                                                                      <  1:256424/140‑1 (MQ=255)

                                                 gACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGcc                                                                                   >  2:617332/1‑140 (MQ=255)

                                                      ctTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTc                                                                                       <  2:686710/131‑1 (MQ=255)

                                                      ctTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTc                                                                                       >  1:686710/1‑131 (MQ=255)

                                                      ctTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTg                                                                              >  1:641566/1‑140 (MQ=255)

                                                      ctTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTg                                                                              >  1:762127/1‑140 (MQ=255)

                                                            aTTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCggg                                                                        <  2:493115/140‑1 (MQ=255)

                                                             ttACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGc                                                                       <  2:834115/140‑1 (MQ=255)

                                                                 tttGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTg                                                                     >  1:292280/1‑138 (MQ=255)

                                                                 tttGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTg                                                                     <  2:292280/138‑1 (MQ=255)

                                                                   tGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTAc                                                                 >  2:493245/1‑140 (MQ=255)

                                                                          ttCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGa                                                          >  1:787287/1‑140 (MQ=255)

                                                                               catGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGc                                                     >  1:89490/1‑140 (MQ=255)

                                                                                 tGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCg                                                           <  1:882756/132‑1 (MQ=255)

                                                                                 tGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCg                                                           >  2:882756/1‑132 (MQ=255)

                                                                                 tGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCAt                                                   <  2:641566/140‑1 (MQ=255)

                                                                                     aaTCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCg                                               <  1:511190/140‑1 (MQ=255)

                                                                                     aaTCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCg                                               >  1:1029227/1‑140 (MQ=255)

                                                                                     aaTCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCg                                               <  1:734137/140‑1 (MQ=255)

                                                                                      aTCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCgg                                              >  1:976185/1‑140 (MQ=255)

                                                                                       tCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGa                                             >  1:4289/1‑140 (MQ=255)

                                                                                            cTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAAtttt                                        >  1:980013/1‑140 (MQ=255)

                                                                                             tGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTa                                       >  1:321304/1‑140 (MQ=255)

                                                                                                  cAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACcgg                                  <  2:787287/140‑1 (MQ=255)

                                                                                                     gCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACcggcgg                               <  2:321304/140‑1 (MQ=255)

                                                                                                         ttGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACg                           >  1:947350/1‑140 (MQ=255)

                                                                                                         ttGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACg                           >  2:986494/1‑140 (MQ=255)

                                                                                                         ttGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACg                           >  1:624031/1‑140 (MQ=255)

                                                                                                         ttGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGATGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACg                           >  2:712587/1‑140 (MQ=255)

                                                                                                          tGCGTTGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGc                          >  1:548076/1‑140 (MQ=255)

                                                                                                               tGGGCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGaa                     <  2:1029227/140‑1 (MQ=255)

                                                                                                                 ggCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACt                   >  1:959645/1‑140 (MQ=255)

                                                                                                                  gCATTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTg                  <  2:1074468/140‑1 (MQ=255)

                                                                                                                    aTTATCGCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGgt                <  2:947350/140‑1 (MQ=255)

                                                                                                                          gCCTTTATCGCTGGCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGGTGTGGAt          <  2:976185/140‑1 (MQ=255)

                                                                                                                                  cGCTGGCTTGGATATGTTTGACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGGTGTGGATGGGGCTgg  >  1:64479/1‑140 (MQ=255)

                                                                                                                                      ggCTTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCTTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGGTGTGGa           <  2:75192/127‑1 (MQ=255)

CGCTGGGGTGGAATGCTTCGTTCAGGGCGTCCCGACAGAGCCTGCTGTGGACCTCTTTAAATTACTTTGAGGGATTCATCATGGAAATCAGCCTGTTGCAGGCATTTGCGTTGGGCATTATCGCCTTTATCGCTGGCCTGGATATGTTTAACGGCCTAACCCATATGCACCGCCCGGTGGTCCTCGGCCCGTTGGTCGGGCTGGTACTTGGCGATCTGCATACCGGAATTTTAACCGGCGGTACGCTGGAACTGGTGTGGATGGGGCTGG  >  NC_000913/3280621‑3280890

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