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
A12 F60 I0 R2	105	83.0	3386788	97.3%	3295344	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,362,578	G→T	27.8%	noncoding (49/76 nt)	pheU ←	tRNA‑Phe

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,362,578	0	G	T	27.8%	103.3 / 35.0	54	noncoding (49/76 nt)	pheU	tRNA‑Phe
Reads supporting (aligned to +/- strand): ref base G (18/21); new base T (5/10); total (23/31)
Fisher's exact test for biased strand distribution p-value = 5.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATC  >  NC_000913/4362448‑4362712

gaATCTGGTTGAGTTCGGTAGAATTGATGTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACgggg                                                                                                                               <  1:259110/140‑1 (MQ=255)

   tCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAAAGATTAAATCGTGTCGTACTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGTACCAAGGACACGGGGAtt                                                                                                                            >  2:692480/1‑140 (MQ=39)

           aGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATcc                                                                                                                    >  1:1210854/1‑140 (MQ=255)

            gTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATccc                                                                                                                   <  2:1526298/140‑1 (MQ=255)

            gTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATccc                                                                                                                   <  2:516552/140‑1 (MQ=255)

            gTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATccc                                                                                                                   <  2:517530/140‑1 (MQ=255)

             ttCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATcccc                                                                                                                  >  2:429259/1‑140 (MQ=255)

             ttCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATcccc                                                                                                                  >  2:432565/1‑140 (MQ=255)

             ttCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATcccc                                                                                                                  >  2:1210336/1‑140 (MQ=255)

              tCGGTAGAATTGATTTGTAGTCAGAACGCTTAAATCGTGGCGTCCTGAAACGAACAACGGACCTCCGAGGAGGTCCGTTTATTTGTATTTGGTGCCCGGACTCGGAATCGAACCAAGCCCACGGGGATTTTCAATCCCCt                                                                                                                 <  2:848382/140‑1 (MQ=37)

              tCGGTAGAATTGAATTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCACCGATGAGGTCCGTGTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCt                                                                                                                 <  2:1098801/140‑1 (MQ=37)

               cGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTg                                                                                                                <  1:1375119/140‑1 (MQ=255)

                       ttGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCg                                                                                                        <  2:778527/140‑1 (MQ=255)

                       atGATATGGAGGCAGCACGCTTATATCGTGGCGTCCTGAAACGAAATCCGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCg                                                                                                        <  2:776512/139‑1 (MQ=37)

                        tGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGa                                                                                                       <  2:811597/140‑1 (MQ=255)

                          aTTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACt                                                                                                     >  2:656661/1‑140 (MQ=255)

                               gAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCt                                                                                                <  1:1199410/140‑1 (MQ=255)

                               gAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCt                                                                                                <  1:1199208/140‑1 (MQ=255)

                               gAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCt                                                                                                >  2:1459888/1‑140 (MQ=255)

                                 ggCAGAACGCTTAATTCGTGGCGTCCTGACACGCACAACGGACCTCCGTGGAGGTCCGTTTATCTGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCGGCTCTACCGACTGAGCTAt                                                                                              <  2:91444/140‑1 (MQ=25)

                                                  gTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCa                                                                             <  1:241900/140‑1 (MQ=255)

                                                   tGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCAt                                                                            >  1:1520125/1‑140 (MQ=255)

                                                   tGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGATCTACCGACTGAGCTATCCGGGCAACGGGGCGCAt                                                                            >  1:453538/1‑140 (MQ=255)

                                                    ggCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGGTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGTGCTATCCGGGCAACGGGGCGCCtt                                                                           >  1:986827/1‑140 (MQ=255)

                                                            gAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGATTTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCTACGGGGCGCATTTAACCGTa                                                                   <  1:1409418/140‑1 (MQ=255)

                                                            gAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTa                                                                   <  2:1110120/140‑1 (MQ=255)

                                                            gAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTa                                                                   <  1:257083/140‑1 (MQ=255)

                                                            gAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTa                                                                   <  1:256943/140‑1 (MQ=255)

                                                                            cTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACTCGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTc                                                   <  1:993003/140‑1 (MQ=255)

                                                                                    aGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAAt                                           <  1:1204718/140‑1 (MQ=255)

                                                                                      gTCCGTTTATATTAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAAttt                                         >  1:696212/1‑140 (MQ=255)

                                                                                      gTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAAGGGGGCGCATTAATCCGTAATCTGCTCATCTCGTCAACATAAttt                                         >  2:496995/1‑140 (MQ=255)

                                                                                       tCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTc                                        >  1:1147493/1‑140 (MQ=255)

                                                                                         cGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAg                                      >  1:707432/1‑140 (MQ=255)

                                                                                         cGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAg                                      >  1:1312032/1‑140 (MQ=255)

                                                                                                   aaTTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGAt                            >  1:1414988/1‑140 (MQ=255)

                                                                                                   aaTTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGAt                            >  1:221980/1‑140 (MQ=255)

                                                                                                     tttGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTc                          >  1:79815/1‑140 (MQ=255)

                                                                                                     tttGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTc                          >  1:79707/1‑140 (MQ=255)

                                                                                                     tttGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTc                          <  1:654418/140‑1 (MQ=255)

                                                                                                     tttGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTc                          >  1:306627/1‑140 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  1:1018116/140‑1 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  2:55902/140‑1 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  1:684753/140‑1 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  1:1459888/140‑1 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  2:1407211/140‑1 (MQ=255)

                                                                                                       tGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCACTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  2:1406606/140‑1 (MQ=255)

                                                                                                       tGGGGCCCGGACTCGGAATCGAACCTAGGTCACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCaa                        <  2:1642917/140‑1 (MQ=255)

                                                                                                                    cGGAATCGAACCAAGGACACGGGGATTGTCAATCCCCTGCTCTACCGACTGAGCGATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTg           <  2:634130/140‑1 (MQ=255)

                                                                                                                      gAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCACCGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCg         >  1:424577/1‑140 (MQ=255)

                                                                                                                      gAATCGAACCAAGGACACGGGGATTTTCAAACCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTAGTCAACCTAATTTCAGTAAAAGCGATTCAACAGCTTAAGATTGCg         >  1:2697/1‑140 (MQ=255)

                                                                                                                       aaTCGAACCAATGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCgg        <  1:1413513/140‑1 (MQ=255)

                                                                                                                            aaCCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAAt   <  2:544405/140‑1 (MQ=255)

                                                                                                                             aCCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATc  >  2:104605/1‑140 (MQ=255)

GAATCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATC  >  NC_000913/4362448‑4362712

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 11 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A