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 F48 I1 R1	76	74.1	2532288	99.0%	2506965	139.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	89,103	G→T	intergenic (+71/‑531)	cra → / → mraZ	DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	89,103	0	G	T	100.0%	198.6 / NA	55	intergenic (+71/‑531)	cra/mraZ	DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (28/27); total (28/27)

GCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATG  >  NC_000913/88966‑89237

gCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCt                                                                                                                                      >  1:548654/1‑140 (MQ=255)

gCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCt                                                                                                                                      <  1:289695/140‑1 (MQ=255)

    aaaCCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTaaa                                                                                                                                  <  1:779649/140‑1 (MQ=255)

         tGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACTTCAATATTCTTAAAGTaaa                                                                                                                             <  2:1176444/140‑1 (MQ=255)

         tGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTaaa                                                                                                                             <  2:636569/140‑1 (MQ=255)

         tGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTaaa                                                                                                                             <  1:731034/140‑1 (MQ=255)

         tGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTaaa                                                                                                                             <  1:464861/140‑1 (MQ=255)

          ggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAAt                                                                                                                            >  2:108626/1‑140 (MQ=255)

          ggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAAt                                                                                                                            <  1:238300/140‑1 (MQ=255)

          ggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAAt                                                                                                                            <  1:36801/140‑1 (MQ=255)

                 cgcgCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTa                                                                                                                     >  2:195926/1‑140 (MQ=255)

                     cATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTcc                                                                                                                 >  2:287718/1‑140 (MQ=255)

                     cATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTcc                                                                                                                 >  1:464976/1‑140 (MQ=255)

                     cATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTcc                                                                                                                 >  1:13933/1‑140 (MQ=255)

                     cATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTcc                                                                                                                 >  1:1166770/1‑140 (MQ=255)

                        tAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTATGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGa                                                                                                              <  2:1008587/140‑1 (MQ=255)

                           aCGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACta                                                                                                           <  2:13933/140‑1 (MQ=255)

                           aCGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACta                                                                                                           <  1:108626/140‑1 (MQ=255)

                             gTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACtatt                                                                                                         <  2:909814/140‑1 (MQ=255)

                              tAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACtatta                                                                                                        <  2:1166770/140‑1 (MQ=255)

                                      aTCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATaaa                                                                                                <  1:195926/140‑1 (MQ=255)

                                      aTCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATaaa                                                                                                >  2:813210/1‑140 (MQ=255)

                                       tCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAAt                                                                                               <  2:548654/140‑1 (MQ=255)

                                        cgccgcGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATg                                                                                              >  1:38513/1‑140 (MQ=255)

                                                         ccGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGt                                                                             >  1:535463/1‑140 (MQ=255)

                                                            tAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGttaa                                                                          >  1:998743/1‑140 (MQ=255)

                                                                  aGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACt                                                                    <  2:998743/140‑1 (MQ=255)

                                                                   gCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTc                                                                   >  2:1020508/1‑140 (MQ=255)

                                                                   gCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTc                                                                   >  1:60449/1‑140 (MQ=255)

                                                                   gCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTc                                                                   <  2:447793/140‑1 (MQ=255)

                                                                   gCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTc                                                                   >  1:188674/1‑140 (MQ=255)

                                                                       cgAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCa                                                               >  2:849654/1‑140 (MQ=255)

                                                                         aaCAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGc                                                             >  1:321960/1‑140 (MQ=255)

                                                                           aaaaaaTACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTg                                                           <  2:595959/139‑1 (MQ=255)

                                                                                  aCGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTca                                                    <  2:38513/140‑1 (MQ=255)

                                                                                     cgcCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACaa                                                 >  2:935586/1‑140 (MQ=255)

                                                                                      gcCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACaat                                                >  1:847214/1‑140 (MQ=255)

                                                                                        cAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACaataa                                              >  1:1194964/1‑140 (MQ=255)

                                                                                          ggTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAAtt                                            <  2:652837/140‑1 (MQ=255)

                                                                                                     ctctGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCg                                 >  2:1001780/1‑140 (MQ=255)

                                                                                                      tctGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGa                                >  2:1211505/1‑140 (MQ=255)

                                                                                                      tctGGCGCGTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGa                                <  2:847214/140‑1 (MQ=255)

                                                                                                            gcgTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAgcgc                          <  1:813210/140‑1 (MQ=255)

                                                                                                              gTAGAGTACGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGt                        <  2:13441/140‑1 (MQ=255)

                                                                                                                     aCGGGACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATCAAGTGATATCGACAGCGCGTTTTTGCa                 <  1:920203/140‑1 (MQ=255)

                                                                                                                         gACTGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCattat             >  1:557030/1‑140 (MQ=255)

                                                                                                                            tGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTAtttt          <  2:321960/140‑1 (MQ=255)

                                                                                                                            tGGACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTAtttt          >  2:1181409/1‑140 (MQ=255)

                                                                                                                              gACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGt        >  2:246142/1‑140 (MQ=255)

                                                                                                                              gACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGt        >  2:329279/1‑140 (MQ=255)

                                                                                                                              gACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGt        >  1:739707/1‑140 (MQ=255)

                                                                                                                              gACATCAATATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGt        >  1:378416/1‑140 (MQ=255)

                                                                                                                              gACATCAATATTCTTAAAGTAAATAAGACTATACCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGt        >  1:1139482/1‑140 (MQ=255)

                                                                                                                                    aaTATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATg  <  2:1181527/140‑1 (MQ=255)

                                                                                                                                    aaTATTCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATg  <  1:849654/140‑1 (MQ=255)

GCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATG  >  NC_000913/88966‑89237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A