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
A21 F5 I0 R1	24	41.2	1474486	89.7%	1322613	148.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,110,747	G→T	28.7%	intergenic (+62/+784)	cdh → / ← yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,110,747	0	G	T	28.7%	66.5 / 21.9	49	intergenic (+62/+784)	cdh/yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (12/22); new base T (6/8); total (18/31)
Fisher's exact test for biased strand distribution p-value = 7.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCA  >  NC_000913_3_pae_tpiA/4110599‑4110890

ttGCTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAggcg                                                                                                                                                  >  1:451084/1‑149 (MQ=255)

  gCTGCCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCCAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAggctgc                                                                                                                                                <  1:18839/149‑1 (MQ=255)

           acaACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCcgcg                                                                                                                                       >  2:391655/1‑149 (MQ=255)

            caACGAAATCTACTGACGGTTAACCGTGCTTCAGGCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGGCAGACTTAAGGCGGCCCCGCCGCGa                                                                                                                                      <  2:266846/149‑1 (MQ=255)

              aCGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGc                                                                                                                                    >  1:87828/1‑149 (MQ=255)

               cGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGCGACTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGAATTAAGGCGGCCCCGCcgcgcgcg                                                                                                                                   >  2:338571/1‑149 (MQ=255)

                caaaTCTAGTGACGCTTAACCGTGCTTCAGCCAAAGAAATTCAGGATCATCAGTCGGAGATTTTGCGTTAAGGCGTAGAGTTAATGAAAGTAAGTGCCGGATATGATATTCTCCGCCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCgg                                                                                                                                  <  2:559644/148‑1 (MQ=255)

                   aTCTATTGACGCGTAACCGTGTTTCAGCCGAGGAAAATCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGCGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGttt                                                                                                                               <  2:584173/149‑1 (MQ=255)

                   aTCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGttt                                                                                                                               <  1:485408/149‑1 (MQ=255)

                    tCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTc                                                                                                                              >  1:24612/1‑149 (MQ=255)

                          gACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAAt                                                                                                                        >  1:446133/1‑149 (MQ=255)

                           aCGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCAGCGAGCGGATTCGCCAAtc                                                                                                                       >  1:375708/1‑148 (MQ=255)

                            cGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTc                                                                                                                      <  2:356937/149‑1 (MQ=255)

                             gCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATGTTGCGTTAAGGCGAGGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCACCGCCAGCGGTTTCGCCACTTCt                                                                                                                     >  1:647631/1‑149 (MQ=255)

                              cTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGCTTATGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTCTCAGACTAGTGGCTGCCCCGCCGCGAGCGGTTTCGGCAATTCTa                                                                                                                    >  1:503275/1‑149 (MQ=255)

                               ttAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAACTCTaa                                                                                                                   >  1:105377/1‑149 (MQ=255)

                                 aaCAGTGCTGCAGCCGAGGAAATTCAGGATCATCAGTGTGGGGTGTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGCTATGAAATGCGGCACCGGCCAGAATTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGa                                                                                                                 <  2:449718/149‑1 (MQ=255)

                                  cccGTTCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGAt                                                                                                                <  2:110115/148‑1 (MQ=255)

                                       gCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTaa                                                                                                           <  1:159297/149‑1 (MQ=255)

                                       gCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTaa                                                                                                           <  1:159388/149‑1 (MQ=255)

                                         ttCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑Ga                                                                                                        <  2:191254/149‑1 (MQ=255)

                                              ccGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATgg                                                                                                   <  1:490288/149‑1 (MQ=255)

                                              ccGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATgg                                                                                                   <  1:392780/149‑1 (MQ=255)

                                              ccGAGGAAACTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATgg                                                                                                   <  1:8506/149‑1 (MQ=255)

                                                gAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATCTGAAATCAGACACCTGTAGCACTTAAGACTACTCCGCCGCGAGCGGTTTCGCCAATTCTACGAACTTGA‑GCTATgtgc                                                                                                 >  2:146338/1‑146 (MQ=255)

                                                gAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGt                                                                                                 >  2:694798/1‑149 (MQ=255)

                                                     aaTTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCGGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCtttt                                                                                            <  1:468253/149‑1 (MQ=255)

                                                                 tcaGTGTGAGGTTTTGCGTTAAGGAAAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCt                                                                                <  1:513884/149‑1 (MQ=255)

                                                                    gtgtGATATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCTGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTgcg                                                                             <  1:304321/149‑1 (MQ=255)

                                                                     tgtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAAGCCGCGTTTCGCCTAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTgcgc                                                                            <  1:692271/149‑1 (MQ=255)

                                                                     tgtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGAAACATGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GCTCTGGGTCGTTGGCTTTCACggagccgc                                                                            >  2:132940/1‑143 (MQ=255)

                                                                      gtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCt                                                                           <  1:40262/149‑1 (MQ=255)

                                                                       tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTCATGCGGCCCCGCCGCGCGCCCTTTAGCCGCTTCGCAG‑TATTAATGGAATGGGGCATTTGCCATCACTGCTGCCCtt                                                                          >  2:77776/1‑149 (MQ=255)

                                                                         agaTTTTGCGGTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCTGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACCGCTGCACTTGc                                                                        <  2:342981/149‑1 (MQ=255)

                                                                           aTTTTGCTTCAAGGGGAAGAGTTAAGGAAAGTAAGTGGCGGATAGGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                      <  2:16047/149‑1 (MQ=255)

                                                                               tgctgtAAGGCGAAGAGTTAAGGAAAGTAAGTGTCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCaa                                                                  <  1:700755/144‑1 (MQ=255)

                                                                                 cGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAaca                                                                <  1:575833/149‑1 (MQ=255)

                                                                                    tAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATACGGCACCTGTCAGACTTACGGCGGCACGGCCGCGAGCGGATTCGCCACTCGTCAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGATTGCCCGCAACACTc                                                             >  2:445222/1‑149 (MQ=255)

                                                                                         cGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTc                                                        <  1:1362/149‑1 (MQ=255)

                                                                                                   aGGAAAGTAAGCGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATCTGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGACtt                                              >  1:458542/1‑149 (MQ=255)

                                                                                                     gAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCAGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATCTGGGTCGTTTGCCTTCACGGCGGCGCTTGCAAGCAACACACCCCTCGTGCCGaagtta                                            >  1:41410/1‑144 (MQ=255)

                                                                                                           aagtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGcgcg                                      <  2:101036/149‑1 (MQ=255)

                                                                                                            agtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCgg                                     <  2:596491/149‑1 (MQ=255)

                                                                                                              cgCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCt                                   <  1:456202/148‑1 (MQ=255)

                                                                                                                   gacatGAAATCGGTCACCGGTCAGGCTTAAGGAGGCCCTGCCGTGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAAc                              <  2:114445/146‑1 (MQ=255)

                                                                                                                   gATATGAAATCCGGCACCTGTCAGACTGAAGGCGGTCTCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGTTCTTTTGCCTTCACTGCTGCGCTTGCCAGCAACACTCCCCTCTTGCCGAGTTTAAGCGCGGCTTCAAc                              <  2:119092/149‑1 (MQ=255)

                                                                                                                      atGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTc                           <  1:149582/149‑1 (MQ=255)

                                                                                                                       tGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCCCGTGCCGAGTTTAAGCGCGGCTGCACCGTcc                          >  2:599831/1‑149 (MQ=255)

                                                                                                                                      gTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATa           <  1:391655/149‑1 (MQ=255)

                                                                                                                                       tCAGACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCATTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAACCGCGGCTTCAACATCCTCTCCGCTCTCAAtcc          >  2:376732/1‑147 (MQ=255)

                                                                                                                                               aaGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCa  <  1:694798/149‑1 (MQ=255)

TTGCTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAA‑GATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCA  >  NC_000913_3_pae_tpiA/4110599‑4110890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A