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 F50 I2 R1	209	44.2	1360995	98.7%	1343302	150.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,214,838	T→C	E213G (GAA→GGA)	bluF ←	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,214,838	0	T	C	98.1%	185.2 / ‑3.6	52	E213G (GAA→GGA)	bluF	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (23/28); total (24/28)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01

TTTCATTAAGTAAAAAAGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTTCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGAAAGGGCA  >  NC_000913/1214692‑1214984

tttCATTAAGTAAAAAAGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCcccc                                                                                                                                                >  1:616853/1‑151 (MQ=255)

    aTTAAGTAAAAAAGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCt                                                                                                                                            <  1:199480/151‑1 (MQ=255)

      tAAGTAAAAAAGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCttt                                                                                                                                          >  2:591401/1‑151 (MQ=255)

           aaaaaaGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCt                                                                                                                                     >  1:367571/1‑151 (MQ=255)

            aaaaaGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTg                                                                                                                                    >  2:178030/1‑151 (MQ=255)

                   gaCTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAAcc                                                                                                                             <  1:52959/151‑1 (MQ=255)

                       gCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGc                                                                                                                           <  1:104292/149‑1 (MQ=255)

                       gCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCt                                                                                                                          <  1:278519/150‑1 (MQ=255)

                        cGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTAt                                                                                                                        >  1:565790/1‑151 (MQ=255)

                             ggTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTg                                                                                                                   <  2:435095/151‑1 (MQ=255)

                                  gTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATggg                                                                                                              <  2:349041/151‑1 (MQ=255)

                                    tAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCt                                                                                                            >  1:121214/1‑151 (MQ=255)

                                     aaCCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCt                                                                                                            <  1:357259/150‑1 (MQ=255)

                                         aGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCtt                                                                                                       <  1:111232/151‑1 (MQ=255)

                                          gggTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTc                                                                                                      <  2:487927/151‑1 (MQ=255)

                                           ggTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTc                                                                                                      >  2:475317/1‑150 (MQ=255)

                                              cATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCAtt                                                                                                   <  2:4174/150‑1 (MQ=255)

                                               aTAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCAtttt                                                                                                 <  1:386131/151‑1 (MQ=255)

                                                tAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCAttttt                                                                                                >  2:57890/1‑151 (MQ=255)

                                                 aGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCAtttttt                                                                                               >  2:137174/1‑151 (MQ=255)

                                                       tAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGcac                                                                                          >  1:577774/1‑150 (MQ=255)

                                                            tgattgaAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATgg                                                                                     <  1:611355/150‑1 (MQ=255)

                                                             gattgaAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCt                                                                                   <  1:43179/151‑1 (MQ=255)

                                                                tgaAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTc                                                                                 <  1:309080/150‑1 (MQ=255)

                                                                            aTCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTAt                                                                     <  2:661825/150‑1 (MQ=255)

                                                                             tCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATcc                                                                   >  2:464480/1‑151 (MQ=255)

                                                                                   aGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCcgcg                                                             <  1:404189/151‑1 (MQ=255)

                                                                                    gCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCcgcg                                                             >  1:318810/1‑150 (MQ=255)

                                                                                    gCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCcgcg                                                             >  2:413990/1‑150 (MQ=255)

                                                                                       cAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATa                                                          >  1:562565/1‑150 (MQ=255)

                                                                                           tGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAggg                                                      >  1:131206/1‑150 (MQ=255)

                                                                                              gtgtGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCg                                                  <  1:364143/151‑1 (MQ=255)

                                                                                                  gCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTAAGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACaa                                              <  1:348755/151‑1 (MQ=255)

                                                                                                     aTCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAAt                                             >  1:91748/1‑149 (MQ=255)

                                                                                                      tCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAgg                                          >  2:511624/1‑151 (MQ=255)

                                                                                                              gCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAg                                   <  1:177802/150‑1 (MQ=255)

                                                                                                                aaGCGCCTTCCTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCa                                <  2:438655/151‑1 (MQ=255)

                                                                                                                  gcgcCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCTGCCGCGATAAGGGATCGACAATAGGATGAAAGGCaa                               >  2:26836/1‑150 (MQ=255)

                                                                                                                    gcCTTACTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGt                            >  1:203178/1‑151 (MQ=255)

                                                                                                                         aCTTTTGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTc                        <  1:87873/150‑1 (MQ=255)

                                                                                                                            tttGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGt                      <  1:189734/149‑1 (MQ=255)

                                                                                                                              tGAGATCCGCTGTGTAGATTTCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTtat                  >  1:131037/1‑151 (MQ=255)

                                                                                                                              tGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTtat                  >  2:534896/1‑151 (MQ=255)

                                                                                                                              tGAGATCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTta                   <  1:511638/150‑1 (MQ=255)

                                                                                                                               gagaTCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTtat                  >  2:11829/1‑150 (MQ=255)

                                                                                                                                  aTCCGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGtt              >  1:288564/1‑151 (MQ=255)

                                                                                                                                    ccGCTGTGTAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTg             <  1:363536/150‑1 (MQ=255)

                                                                                                                                         gtgtAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGaaa       <  2:532529/151‑1 (MQ=255)

                                                                                                                                         gtgtAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGa         <  2:474128/149‑1 (MQ=255)

                                                                                                                                            tAGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGAAAggg    >  2:12806/1‑151 (MQ=255)

                                                                                                                                             aGATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGAAAggg    <  1:58889/150‑1 (MQ=255)

                                                                                                                                              gATTCCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGAAAGGGca  <  1:645877/151‑1 (MQ=255)

TTTCATTAAGTAAAAAAGAGACTGCGTCAGGTTCGTTAACCAGGGTCATAGGTAATAGATTGATTGAAATCATTTTATCACCGAGCTCAAGTGCGTGTGCCATCGTGAATGCAAGCGCCTTACTTTTGAGATCCGCTGTGTAGATTTCCCCGTCTTTACGCTGCCCAACCGCTATGGCTGATGGGCTATCTTCATTTTTTTGCACAATGGCTTCAAAAGCGATTATCCGCCGCGATAAGGGATCGACAATAGGATGAAAGGCAAAGTGGTCGTTTATAGTTGGTGAAAGGGCA  >  NC_000913/1214692‑1214984

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A