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
A5 F28 I1 R1	260	73.5	2514320	99.3%	2496719	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,822,657	A→G	E86E (GAA→GAG)	spoT →	bifunctional (p)ppGpp synthase/hydrolase SpoT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,822,657	0	A	G	100.0%	212.3 / NA	59	E86E (GAA→GAG)	spoT	bifunctional (p)ppGpp synthase/hydrolase SpoT
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (32/27); total (32/27)

TGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCCGC  >  NC_000913/3822525‑3822792

tGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCttt                                                                                                                                  <  1:363668/140‑1 (MQ=255)

      cTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTa                                                                                                                            >  2:530531/1‑140 (MQ=255)

            cACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCg                                                                                                                      >  1:699914/1‑140 (MQ=255)

            cACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCg                                                                                                                      >  1:1162455/1‑140 (MQ=255)

              cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc                                                                                                                    >  1:558550/1‑140 (MQ=255)

              cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc                                                                                                                    >  1:508173/1‑140 (MQ=255)

              cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc                                                                                                                    >  1:179434/1‑140 (MQ=255)

              cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc                                                                                                                    >  1:1244519/1‑140 (MQ=255)

               gCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCg                                                                                                                   >  2:370235/1‑140 (MQ=255)

                  cccGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCg                                                                                                                <  1:1191523/140‑1 (MQ=255)

                  cccGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCg                                                                                                                <  1:385865/140‑1 (MQ=255)

                    cGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAg                                                                                                              <  2:1162455/140‑1 (MQ=255)

                     ggTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGc                                                                                                             >  2:738876/1‑140 (MQ=255)

                            gctGCCTGCATTCTGGCCGAGATGAAACTCGCCTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTaga                                                                                                      <  1:786898/138‑1 (MQ=255)

                                ccTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAgggg                                                                                                  <  1:156989/140‑1 (MQ=255)

                                 cTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAggggg                                                                                                 >  1:144005/1‑140 (MQ=255)

                                       tCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAggg                                                                                                   >  1:793251/1‑132 (MQ=255)

                                       tCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAggg                                                                                                   <  2:793251/132‑1 (MQ=255)

                                           gCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACt                                                                                       >  2:707374/1‑140 (MQ=255)

                                            ccGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACtt                                                                                      >  2:444027/1‑140 (MQ=255)

                                              gagaTGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGa                                                                                    <  1:1146947/140‑1 (MQ=255)

                                                     aaCTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTc                                                                             >  1:404593/1‑140 (MQ=255)

                                                           aCTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTc                                                                       <  2:558550/140‑1 (MQ=255)

                                                           aCTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTc                                                                       >  2:673337/1‑140 (MQ=255)

                                                            cTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTACAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTcc                                                                      >  2:60108/1‑140 (MQ=255)

                                                            cTATGAAACGCTGATAGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGC‑TTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCcg                                                                     <  1:113510/140‑1 (MQ=255)

                                                                gAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGa                                                                  <  1:707374/140‑1 (MQ=255)

                                                                       tGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATaagaaa                                                           <  2:1244519/140‑1 (MQ=255)

                                                                                   tgctgcATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGcc                                               >  1:1012662/1‑140 (MQ=255)

                                                                                             catGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTc                                     >  1:1023025/3‑140 (MQ=255)

                                                                                             cGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTc                                     >  2:347816/1‑140 (MQ=255)

                                                                                             cGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTc                                     >  2:654077/1‑140 (MQ=255)

                                                                                              gTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCg                                    <  1:488009/140‑1 (MQ=255)

                                                                                               tGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGc                                   >  1:520051/1‑140 (MQ=255)

                                                                                               tGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGc                                   >  1:802591/1‑140 (MQ=255)

                                                                                               tGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGc                                   <  1:849947/140‑1 (MQ=255)

                                                                                                  ttGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAg                                >  2:217114/1‑140 (MQ=255)

                                                                                                          aCTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTAt                        >  2:285736/1‑140 (MQ=255)

                                                                                                           cTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATg                       >  1:199034/1‑140 (MQ=255)

                                                                                                           cTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATg                       >  1:1031209/1‑140 (MQ=255)

                                                                                                            tCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATgg                      <  2:1012662/140‑1 (MQ=255)

                                                                                                            tCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATgg                      >  1:354613/1‑140 (MQ=255)

                                                                                                             cccGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGc                     >  1:500880/1‑140 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  1:444027/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  2:199034/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  1:1003184/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  2:404593/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  1:347816/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  1:275906/140‑1 (MQ=255)

                                                                                                               cGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGa                   <  1:217114/140‑1 (MQ=255)

                                                                                                                gCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAg                                >  2:252551/1‑126 (MQ=255)

                                                                                                                gCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAg                                <  1:252551/126‑1 (MQ=255)

                                                                                                                gCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGAt                  <  2:1031209/140‑1 (MQ=255)

                                                                                                                    ccTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTg              <  2:179434/140‑1 (MQ=255)

                                                                                                                    ccTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTg              <  2:699914/140‑1 (MQ=255)

                                                                                                                    ccTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTg              <  1:654077/140‑1 (MQ=255)

                                                                                                                               atGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGAAAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCcg   >  2:867411/1‑140 (MQ=255)

                                                                                                                               atGGAGCAACTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCcg   >  1:785187/1‑140 (MQ=255)

                                                                                                                                tGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCcgc  >  1:597506/1‑140 (MQ=255)

TGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCCGC  >  NC_000913/3822525‑3822792

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