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
A4 F67 I0 R1	279	64.3	2479458	95.9%	2377800	135.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,221,494	G→T	20.9%	S112I (AGC→ATC)	ygjJ →	putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,221,494	0	G	T	20.9%	104.7 / 27.1	57	S112I (AGC→ATC)	ygjJ	putative periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (26/19); new base T (6/6); total (32/25)
Fisher's exact test for biased strand distribution p-value = 7.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

TATTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCACCCCCGATC  >  CP009273/3221384‑3221631

tatTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAAcc                                                                                                              <  2:282832/140‑1 (MQ=255)

tatTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAAcc                                                                                                              <  2:411752/140‑1 (MQ=255)

 atTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCg                                                                                                             >  1:1048293/1‑140 (MQ=255)

 atTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCg                                                                                                             >  1:1033489/1‑140 (MQ=255)

 atTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCg                                                                                                             >  1:5657/1‑140 (MQ=255)

 atTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCg                                                                                                             >  1:504059/1‑140 (MQ=255)

 atTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGCCAGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCg                                                                                                             >  1:598171/1‑140 (MQ=255)

    gAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGttt                                                                                                          >  2:88516/1‑140 (MQ=255)

    gAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGttt                                                                                                          >  2:559866/1‑140 (MQ=255)

    gAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGttt                                                                                                          >  1:453164/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:557202/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:390169/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:390139/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:210317/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:326454/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:286572/1‑140 (MQ=255)

          ggCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGACCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATgg                                                                                                    >  1:44010/1‑140 (MQ=255)

            ccTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCg                                                                                                  <  2:453164/140‑1 (MQ=255)

                gagaTGAAGTACGGCTCCTTGTTCGGCCTGATTTACGGCGAAGGCTGGACCGGGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGGGGAATTAACCGTTTCTATGGCGGTTa                                                                                              <  2:731666/140‑1 (MQ=255)

                gagaTGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTa                                                                                              <  2:649854/140‑1 (MQ=255)

                gagaTGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTa                                                                                              <  2:1044941/140‑1 (MQ=255)

                 agaTGAAGTACGGCTCCTGTTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGTTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTAt                                                                                             <  1:821342/140‑1 (MQ=255)

                 agaTGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTAt                                                                                             <  1:319935/140‑1 (MQ=255)

                  gaTGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATc                                                                                            >  2:1221151/1‑140 (MQ=255)

                   aTGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCg                                                                                           >  2:945128/1‑140 (MQ=255)

                            ggCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAatga                                                                                  <  2:488582/140‑1 (MQ=255)

                                   ggTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCAcc                                                                           >  2:619505/1‑140 (MQ=255)

                                   ggTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCAcc                                                                           >  2:146768/1‑140 (MQ=255)

                                   ggTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCAcc                                                                           >  2:450762/1‑140 (MQ=255)

                                                        aaGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGt                                                      >  2:606872/1‑140 (MQ=255)

                                                        aaGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGt                                                      >  2:792920/1‑140 (MQ=255)

                                                               gACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGAtt                                               <  1:328667/140‑1 (MQ=255)

                                                               gACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGAtt                                               <  1:401956/140‑1 (MQ=255)

                                                                   gTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTc                                           <  2:554003/140‑1 (MQ=255)

                                                                   gTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTc                                           <  2:116284/140‑1 (MQ=255)

                                                                    tGCAGGCCTACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGTGTTGGTATCGAGGTCGGAAATAACCGTTTCTATGGCGGTTATCTTACCAATGATGGCACCGAAATCATCCTCAGTCTGCGTCAGTATTCATCg                                          >  2:572920/1‑140 (MQ=255)

                                                                    tGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCg                                          >  1:408507/1‑140 (MQ=255)

                                                                    tGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCg                                          >  1:255875/1‑140 (MQ=255)

                                                                    tGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCg                                          >  2:479098/1‑140 (MQ=255)

                                                                           cGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATg                                   <  1:996653/140‑1 (MQ=255)

                                                                           cGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATg                                   <  1:898975/140‑1 (MQ=255)

                                                                           cGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATg                                   <  1:626846/140‑1 (MQ=255)

                                                                           cGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATg                                   <  1:207280/140‑1 (MQ=255)

                                                                            gACCACGACGGCAATGCCTGGGTGCCAGACCATAGGTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGa                                  <  2:951368/140‑1 (MQ=255)

                                                                            gACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGa                                  >  2:31601/1‑140 (MQ=255)

                                                                            gACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGa                                  >  2:830112/1‑140 (MQ=255)

                                                                            gACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGa                                  >  2:852434/1‑140 (MQ=255)

                                                                            gACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGa                                  <  1:945128/140‑1 (MQ=255)

                                                                                        aaTGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGACTTAACCGTGTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCGTCGCTGGATGACCTGCAAgggtg                      >  1:131960/1‑140 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:557202/140‑1 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:390169/140‑1 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:390139/140‑1 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:326454/140‑1 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:210317/140‑1 (MQ=255)

                                                                                                       gACCATATCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGAGGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCAcccc       <  2:286572/140‑1 (MQ=255)

                                                                                                            tAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCACCCCCGATc  >  2:379901/1‑140 (MQ=255)

                                                                                                            tAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCACCCCCGATc  >  2:130538/1‑140 (MQ=255)

TATTGAAGGTGGCCTGGAGATGAAGTACGGCTCCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGCAATGGTGGGGCGATTTCACCCCCGATC  >  CP009273/3221384‑3221631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A