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
A15 F60 I1 R1	13	54.8	1858072	98.6%	1832058	139.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,545,052	A→G	intergenic (+23/‑44)	fimC → / → fimD	type 1 fimbriae periplasmic chaperone/type I fimbriae usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,545,052	0	A	G	100.0%	179.8 / NA	47	intergenic (+23/‑44)	fimC/fimD	type 1 fimbriae periplasmic chaperone/type I fimbriae usher protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/26); total (21/26)

CAATGGGCGAAAGCACGGTTAAATTGCCTTCTGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGACTC  >  NC_000913/4544917‑4545185

cAATGGGCGAAAGCACAGTTAACTTGCCTTCCGATGCAGAAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATaa                                                                                                                                   <  2:396166/140‑1 (MQ=255)

   tGGGCGAAAGCACGGTTAAATTGCCTTCTGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGTGAATTTGTCGCCTGGATaaaaa                                                                                                                                >  1:317807/1‑140 (MQ=255)

   tGGGCGAAAGCACGGTTAAATTGCCTTCTGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATaaaaa                                                                                                                                >  1:898803/1‑140 (MQ=255)

       cGAAAGCACGGTTAAATTGCCTTCTGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAAt                                                                                                                            >  2:773362/1‑140 (MQ=255)

                  ttAAATTGCCTTCTGATCCAGGAAGCAATATTACTCACCTAACAATAATTGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCggg                                                                                                                 <  2:284195/140‑1 (MQ=255)

                          ccTTCTGATGCAGGAAGGAATAGTACTTACCAAACCATACATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTa                                                                                                         <  2:317807/140‑1 (MQ=255)

                             tCTGATGCAGGAAGCAATATTACTTACCGAAGAATCAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGc                                                                                                      <  2:324251/140‑1 (MQ=255)

                               tGATGCAGTAAGCAATATTACTGACCGAACAGTGAATGATTATGGCGCTCTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCg                                                                                                    <  2:411167/140‑1 (MQ=255)

                               tGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTGCCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCg                                                                                                    <  2:5648/140‑1 (MQ=255)

                                gATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCgg                                                                                                   <  2:927054/140‑1 (MQ=255)

                                 aTGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCgga                                                                                                  <  1:660455/140‑1 (MQ=255)

                                          gCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAG‑CGGAGGAATAATGt                                                                                        <  1:185208/140‑1 (MQ=255)

                                           cAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                                                                        <  1:712627/140‑1 (MQ=255)

                                             atatTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCa                                                                                      >  1:224831/1‑140 (MQ=255)

                                                ttacttacCGAACAATAAATGACTATGGCGCTCTTGCCCTCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCatat                                                                                   <  2:320464/140‑1 (MQ=255)

                                                      acCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGTGTGATTTAAAGCCGAAGGAATAATGTCATATCTGAAt                                                                             >  1:320464/1‑140 (MQ=255)

                                                      acCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCt                                                                                 <  2:37857/136‑1 (MQ=255)

                                                      acCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCt                                                                                 >  1:37857/1‑136 (MQ=255)

                                                      acCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAt                                                                             >  2:681276/1‑140 (MQ=255)

                                                       ccGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAtt                                                                            >  2:235297/1‑140 (MQ=255)

                                                        cGAACAATAAATGATTTAGGCGCACTTACCGTCAACATGTCGGGCGTACTGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                                                                           <  2:452811/140‑1 (MQ=255)

                                                        cGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                                                                           >  1:180728/1‑140 (MQ=255)

                                                        cGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                                                                           >  1:773771/1‑140 (MQ=255)

                                                                 aaTGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTa                                                                  >  2:495777/1‑140 (MQ=255)

                                                                      ttATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                                                             <  2:831612/140‑1 (MQ=255)

                                                                      ttATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                                                             <  2:773771/140‑1 (MQ=255)

                                                                      ttATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                                                             <  1:235297/140‑1 (MQ=255)

                                                                         tGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaa                                                          >  2:859544/1‑140 (MQ=255)

                                                                          ggCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa                                                         <  2:577391/140‑1 (MQ=255)

                                                                             gcACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacac                                                      >  1:736597/1‑140 (MQ=255)

                                                                               aCTTTCCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacacac                                                    <  1:902997/140‑1 (MQ=255)

                                                                                           aaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCata                                        >  2:516662/1‑140 (MQ=255)

                                                                                           aaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGGCATATCTGCATTTAAGCCTTTACCAGCGAAGCACACAATGCTTGCata                                        >  2:287950/1‑140 (MQ=255)

                                                                                                   gCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTCGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAg                                >  2:195706/1‑140 (MQ=255)

                                                                                                   gCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTCGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAg                                <  1:195706/140‑1 (MQ=255)

                                                                                                     gTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCa                              >  2:142930/1‑140 (MQ=255)

                                                                                                            aaTAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTg                       <  1:516662/140‑1 (MQ=255)

                                                                                                             aTAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTgg                      <  1:773362/140‑1 (MQ=255)

                                                                                                                aCGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAATACACAATTCTTGCAGATTCGTGAGCATCGTTTGGCTg                   >  1:295518/1‑140 (MQ=255)

                                                                                                                 cGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTgg                  >  1:855101/1‑140 (MQ=255)

                                                                                                                      ggggAATTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGttttt             >  2:484594/1‑140 (MQ=255)

                                                                                                                           aTTTTTCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTc        <  2:855101/140‑1 (MQ=255)

                                                                                                                               ttCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGAc    <  2:898803/140‑1 (MQ=255)

                                                                                                                               ttCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGAc    <  1:681276/140‑1 (MQ=255)

                                                                                                                               ttCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGAc    <  2:736597/140‑1 (MQ=255)

                                                                                                                               ttCGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGAc    <  2:180728/140‑1 (MQ=255)

                                                                                                                                 cGCCTGGATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGACTc  >  2:833941/1‑140 (MQ=255)

CAATGGGCGAAAGCACGGTTAAATTGCCTTCTGATGCAGGAAGCAATATTACTTACCGAACAATAAATGATTATGGCGCACTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTTGCATATTCGTAAGCATCGTTTGGCTGGTTTTTTTGTCCGACTC  >  NC_000913/4544917‑4545185

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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