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
A0 F0 I1 R1	16	48.9	1703346	91.6%	1560264	146.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,604,632	C→A	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,604,632	0	C	A	96.2%	160.0 / NA	54	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (1/1); new base A (23/28); total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTA  >  NC_000913_3_pae_tpiA/4604489‑4604773

cgaccgacTGAACAATCAGTGGTACATTAACCAAACCCGGACGTTAAGCCGGACGGAGAGAGAAATATTGCGCTTTATGTAGCGTGCCTACTTAGTTACACAAATTGCCGAGCAGCTTAGACGCAATATCCAAACGCTCCGCGCACATa                                                                                                                                          >  2:334371/1‑149 (MQ=255)

   cggacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAAt                                                                                                                                       <  2:458359/147‑1 (MQ=255)

        tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                  >  1:145574/1‑149 (MQ=255)

        tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                  >  2:126372/1‑149 (MQ=255)

             aaTCAGTGTTACATGAACGAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                             <  2:377314/149‑1 (MQ=255)

             aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGAt                                                                                                                             >  1:720991/1‑149 (MQ=255)

               tCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGt                                                                                                                           >  1:316357/1‑149 (MQ=255)

                   tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGGACATAAATTTAATGTGATGTCGaa                                                                                                                       >  1:815907/1‑149 (MQ=255)

                            aaCCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGt                                                                                                              <  1:126372/149‑1 (MQ=255)

                             aCCACAGCCGGACGTTAAGCCCGACAGAGAGAGAAATCTTGCGCTTTATGTCGCGTGGCTACTCAACGACACAAATTGCCGAGCAGCTTAAACGCAGTATCAAAACGATCCCTGAACATAACATTCTTGGCGTGTCGAAACTggtgtgt                                                                                                             >  2:387399/1‑144 (MQ=255)

                              ccAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGACTACTCAATGACACAAATTGCCGAGCCGCTTACACCCAACACTAAAACGAACCGTGAACAAAAATTTAATGTGATGTCCAAAATGGGCGTCa                                                                                                            >  2:261394/1‑149 (MQ=255)

                               caaattcGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAAAAATTTAATGTGATGTCGAAACTGGGCGTCAg                                                                                                           >  2:651821/7‑149 (MQ=255)

                               cAAAGCCGGACGTTAAGACCGACGGAGAGAGAAATATTGCGCGTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAAACAAATATTAAAACAATCCTGGAACATAAATTTAATGTGATGTCGAAACTGGGCATCAg                                                                                                           >  2:426986/1‑149 (MQ=255)

                                    ccGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAGCATAAAGTTAATGTGATGTCGAAACTGGGCGTCAGTTCTg                                                                                                      >  1:795302/1‑149 (MQ=255)

                                     cgtgccgtAAGCCAGACGGATAGAGAAATAGTGCGCTTTATGGCGTGTGGCTACTCAAGGACACAAATTGCCTAGCAGCTTAAACGCAATATCAAAACGATCTGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGa                                                                                                     <  2:379409/142‑1 (MQ=255)

                                         cGTTAGGCCCGGCGGAGAGAGTAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCa                                                                                                 <  1:75919/149‑1 (MQ=255)

                                         cGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCGATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCCAAACTGGGCGTCAGTTCTGACGCa                                                                                                 >  2:655193/1‑149 (MQ=255)

                                          gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAg                                                                                                <  2:832630/149‑1 (MQ=255)

                                             aaGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACGCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgt                                                                                             >  2:290860/1‑149 (MQ=255)

                                                  cGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGttgttg                                                                                        <  2:498459/149‑1 (MQ=255)

                                                    aCGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                      <  1:736246/149‑1 (MQ=255)

                                                    aCGGAGAGAGAAACATTGCGGTTTTGGTCGCGTGGCTACTCAATGACAAAAAGTGCCGAGCAGCTTAAACGCAATATCAAAACGAGCCGGGAACATAAATTTAATGTGATGTCAAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                      <  2:336925/149‑1 (MQ=255)

                                                     cGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAg                                                                                     <  1:286390/149‑1 (MQ=255)

                                                              aaaTATTGCGCTTTATGTCGCGTGGCTACTCAATGAAACAAAGTACCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGCTGTCGAAACTGGGCGTCGGTTCTGACGCAGGGTTGTTGGAGGCCGCAGat                                                                            >  1:202566/1‑149 (MQ=255)

                                                                 tatTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATAtt                                                                         >  1:593251/1‑149 (MQ=255)

                                                                 tatTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATAtt                                                                         >  1:826517/1‑149 (MQ=255)

                                                                    tGCGGTTTATGTCGCGTGGCTCAGCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTg                                                                      <  2:153968/149‑1 (MQ=255)

                                                                    tGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                      <  1:60616/133‑1 (MQ=255)

                                                                    tGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                      >  2:60616/1‑133 (MQ=255)

                                                                     gcgcTTCATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGt                                                                     <  1:52200/149‑1 (MQ=255)

                                                                       gcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                   <  1:394633/149‑1 (MQ=255)

                                                                        cTTTATGTCGCGTGGCTCCTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtat                                                                  <  1:606421/149‑1 (MQ=255)

                                                                                         aCTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaa                                                 >  1:823525/1‑149 (MQ=255)

                                                                                             aacgccacaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTCGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                             <  1:104626/144‑1 (MQ=255)

                                                                                             aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                             >  2:632455/1‑149 (MQ=255)

                                                                                                 acacAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTg                                                     >  2:570577/1‑137 (MQ=255)

                                                                                                 acacAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTg                                                     <  1:570577/137‑1 (MQ=255)

                                                                                                 acacAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTaa                                         <  1:553623/149‑1 (MQ=255)

                                                                                                         tGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCTGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGc                                 <  1:640215/149‑1 (MQ=255)

                                                                                                           ccGAGCAGCTTAAACGCAATATTAAATCGATCCGCGCACATAAATTTAATGGGATGTGGAAACTGGGCGTCAGTCCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCAt                               <  1:11611/149‑1 (MQ=255)

                                                                                                           ccGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCAt                               <  2:690015/149‑1 (MQ=255)

                                                                                                             gAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCGGCAGATATTCTGTTAGGTATGCGGCATTGCGAAACAAGTAATGTGGTGCATcc                             >  1:663417/1‑149 (MQ=255)

                                                                                                             gAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATcc                             <  1:290860/149‑1 (MQ=255)

                                                                                                                cagcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTa                          <  2:559170/149‑1 (MQ=255)

                                                                                                                 agcTTAACCGCAATAGCAAAACGTTCCGTGAACATAAATTTAATGTGATGTCGAAACTTGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGACATTCGTTTATGTATGCGGCATTGCGAAACAAGTAATGGTTTGCTTCCCTAt                         <  2:102716/149‑1 (MQ=255)

                                                                                                                      aaaCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                   >  1:781635/1‑134 (MQ=255)

                                                                                                                      aaaCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                   >  1:781209/1‑134 (MQ=255)

                                                                                                                      aaaCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                   <  2:781209/134‑1 (MQ=255)

                                                                                                                      aaaCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                   <  2:781635/134‑1 (MQ=255)

                                                                                                                          gCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCa                <  1:512469/149‑1 (MQ=255)

                                                                                                                          gCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAATGGGCGGCAGTTCTGACGCAAGGTTGTTGGACGCCGCAGAGCTTCAGCTATGTATCGCGCATAGCGAAACACGAACTTTGTAGCATGCGTATAAACCCGcg                >  2:29026/1‑148 (MQ=255)

                                                                                                                            gatatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCatg              >  2:438380/2‑149 (MQ=255)

                                                                                                                                      cGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt    <  2:826517/149‑1 (MQ=255)

                                                                                                                                        aTCCGTGAAAATAATTGTAATGTGATGTCGAAACTGGGCGTCAGTTCTGATGTTTGTTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTa  <  2:687232/149‑1 (MQ=255)

CGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTA  >  NC_000913_3_pae_tpiA/4604489‑4604773

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A