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 F50 I2 R1	139	64.5	2139856	92.7%	1983646	149.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,209,439	G→A	pseudogene (340/2001 nt)	yehQ →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,209,439	0	G	A	100.0%	181.4 / NA	50	pseudogene (340/2001 nt)	yehQ	pseudogene
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/27); total (23/27)

TGAAAGAGGCTCAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGGCTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCGCAGCAGTATT  >  NC_000913/2209293‑2209582

tGAAAGAGGCTCAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTAc                                                                                                                                             >  1:648215/1‑151 (MQ=255)

 gAAAGAGGCTCAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTAcc                                                                                                                                            <  2:319691/151‑1 (MQ=255)

 gAAAGAGGCTCAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTAcc                                                                                                                                            <  1:601719/151‑1 (MQ=255)

           cAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGa                                                                                                                                    <  1:881605/149‑1 (MQ=255)

                       ggggCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAAc                                                                                                                      <  2:879959/151‑1 (MQ=255)

                           ccAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACgcgc                                                                                                                  <  2:5279/151‑1 (MQ=255)

                             aaCGGTATGTGTCGTCATCGCGTGATGCTGGAGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGcac                                                                                                                >  2:513719/1‑151 (MQ=255)

                               cGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAg                                                                                                              <  2:724473/151‑1 (MQ=255)

                                      tgCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTgg                                                                                                       >  1:171144/1‑151 (MQ=255)

                                       gCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGt                                                                                                      >  2:924745/1‑151 (MQ=255)

                                                      tGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGGGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGACATCAc                                                                                       >  2:1060950/1‑151 (MQ=255)

                                                       gCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCAc                                                                                       <  2:42342/150‑1 (MQ=255)

                                                          ggTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCAt                                                                                    <  1:915329/150‑1 (MQ=255)

                                                             gtTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGa                                                                                 <  1:401526/150‑1 (MQ=255)

                                                                aaGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAgttg                                                                             >  1:633867/1‑151 (MQ=255)

                                                                  gTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAgttgtt                                                                           <  1:805588/151‑1 (MQ=255)

                                                                   ttATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGTACTGACTACCCTTCCCGATGCTCCCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAgttgtt                                                                           <  2:598122/150‑1 (MQ=255)

                                                                           gACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGcc                                                                  >  2:115541/1‑151 (MQ=255)

                                                                                 gtgCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCggg                                                               >  2:333482/1‑148 (MQ=255)

                                                                                   gCCACCGCTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGaaa                                                          <  2:689806/151‑1 (MQ=255)

                                                                                     caccacTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAAtt                                                        >  1:592799/1‑151 (MQ=255)

                                                                                        cacTCAGTCTACGGAAAAAGAAGAAGAGAGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGAGCGCCGGGTGAAATTccc                                                     >  2:749875/1‑151 (MQ=255)

                                                                                           tCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCctct                                                  >  2:560454/1‑151 (MQ=255)

                                                                                            cAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTg                                                 <  2:436157/151‑1 (MQ=255)

                                                                                            cAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTg                                                 <  1:1036640/151‑1 (MQ=255)

                                                                                             aGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGc                                                >  2:139652/1‑151 (MQ=255)

                                                                                             aGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGc                                                <  2:524295/151‑1 (MQ=255)

                                                                                             aGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGc                                                >  2:1065377/1‑151 (MQ=255)

                                                                                             aGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGc                                                >  2:774841/1‑151 (MQ=255)

                                                                                                  aCGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCGAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCt                                           <  2:601608/151‑1 (MQ=255)

                                                                                                    ggAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCtt                                          >  1:653313/1‑150 (MQ=255)

                                                                                                    ggAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTa                                         <  1:1011581/151‑1 (MQ=255)

                                                                                                       aaaaGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCg                                      >  2:1024225/1‑151 (MQ=255)

                                                                                                             agaagaGTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGc                                <  1:163430/151‑1 (MQ=255)

                                                                                                                   gTGGGATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGAtgtg                          >  2:681834/1‑151 (MQ=255)

                                                                                                                      ggATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGc                         <  1:814251/149‑1 (MQ=255)

                                                                                                                      ggATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGt                       >  2:38775/1‑151 (MQ=255)

                                                                                                                      ggATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGt                       <  1:396092/151‑1 (MQ=255)

                                                                                                                       gATCCGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGtt                      >  2:188813/1‑151 (MQ=255)

                                                                                                                          ccGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGttttt                   <  2:86235/151‑1 (MQ=255)

                                                                                                                          ccGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGttttt                   <  1:765898/151‑1 (MQ=255)

                                                                                                                          ccGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGtttt                    <  1:705780/150‑1 (MQ=255)

                                                                                                                          ccGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGtttt                    <  1:659824/150‑1 (MQ=255)

                                                                                                                           cGGCAATCTGGCTGGAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGttttt                   >  1:817456/1‑150 (MQ=255)

                                                                                                                               aaTCTGGCTGGAAGAACTGACTGCCCTTCCCGATGCGACCCGCAAACGCGCACAGGCGCTGGTCGATCAAGGCAGCACCATTGAGTTGTTCTGTGCGCCGGGTTAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGGGTTTTTAtt                <  2:696074/149‑1 (MQ=255)

                                                                                                                                    ggctggAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCgca          <  2:629383/150‑1 (MQ=255)

                                                                                                                                       tggAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCgcagc        >  2:131913/1‑149 (MQ=255)

                                                                                                                                        ggAAGAACTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCGCAGCAGt     <  2:185540/151‑1 (MQ=255)

                                                                                                                                          aagaaCTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCGCAGCAGTAt   >  2:182691/1‑151 (MQ=255)

                                                                                                                                           agaaCTGACTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCGCAGCAGTAtt  >  1:495706/1‑151 (MQ=255)

TGAAAGAGGCTCAGTGCAGTTGCGGGGCCAACGGTATGTGCCGTCATCGCGTGATGCTGGTGTTAAGTTATCAACGACTTTGTGCCACCACTCAGTCTACGGAAAAAGAAGAAGAGTGGGATCCGGCAATCTGGCTGGAAGAACTGGCTACCCTTCCCGATGCTACCCGCAAACGCGCACAGGCGCTGGTCGCTAAAGGCATCACCATTGAGTTGTTCTGTGCGCCGGGTGAAATTCCCTCTGCCCGCTTACCGATGAGCGATGTGCGTTTTTATTCCCGCAGCAGTATT  >  NC_000913/2209293‑2209582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A