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 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,289,090	A→G	T93A (ACA→GCA)	yraJ →	putative fimbrial usher protein YraJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,289,090	0	A	G	100.0%	160.1 / NA	46	T93A (ACA→GCA)	yraJ	putative fimbrial usher protein YraJ
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (23/23); total (23/23)

GGAAACCACAAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTACATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGC  >  NC_000913/3288963‑3289219

ggAAACCACAAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCa                                                                                                                       <  1:108540/140‑1 (MQ=255)

ggAAACCACAAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCa                                                                                                                       >  1:670557/1‑140 (MQ=255)

   aaCCACAAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATg                                                                                                                    <  2:460799/140‑1 (MQ=255)

      cacaAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGTTTTCACAGAAAAAAATTGCATTTACCGCCAATGCag                                                                                                                 <  1:861204/140‑1 (MQ=255)

      cacaAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGc                                                                                                                         >  2:476338/1‑132 (MQ=255)

      cacaAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGc                                                                                                                         <  1:476338/132‑1 (MQ=255)

                       aaaCAACCGATCTGTCGCGTTTTTCAAAAAAGTATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCca                                                                                                <  1:750699/140‑1 (MQ=255)

                       aaaCAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCca                                                                                                <  1:132963/140‑1 (MQ=255)

                       aaaCAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCca                                                                                                <  2:848128/140‑1 (MQ=255)

                         acaacCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCcaca                                                                                              >  2:256444/1‑140 (MQ=255)

                            acCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGtt                                                                                           <  1:256444/140‑1 (MQ=255)

                            acCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGtt                                                                                           >  2:186248/1‑140 (MQ=255)

                              cGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTa                                                                                         >  1:430280/1‑140 (MQ=255)

                               gATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTAc                                                                                        <  1:2181/140‑1 (MQ=255)

                                aTCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTAc                                                                                        >  1:260985/1‑139 (MQ=255)

                                aTCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTAc                                                                                        <  2:260985/139‑1 (MQ=255)

                                aTCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACg                                                                                       >  2:137021/1‑140 (MQ=255)

                                aTCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACg                                                                                       >  2:124249/1‑140 (MQ=255)

                                 tCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACgg                                                                                      <  2:301858/140‑1 (MQ=255)

                                     tCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAGAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGa                                                                                  >  1:524784/1‑140 (MQ=255)

                                        cgTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGaaca                                                                               >  2:252885/1‑140 (MQ=255)

                                        cgTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGaaca                                                                               <  1:177973/140‑1 (MQ=255)

                                        cgTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGaaca                                                                               <  1:186248/140‑1 (MQ=255)

                                                  aaaaaTATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAg                                                                     <  1:252885/140‑1 (MQ=255)

                                                    aaaTATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCt                                                                   <  1:674210/140‑1 (MQ=255)

                                                              aaCTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAg                                                         >  2:766532/1‑140 (MQ=255)

                                                                          cTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATc                                             >  1:90676/1‑140 (MQ=255)

                                                                          cTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATc                                             >  2:690000/1‑140 (MQ=255)

                                                                          cTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATc                                             >  1:3446/1‑140 (MQ=255)

                                                                                aGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGgcg                                       <  1:137021/140‑1 (MQ=255)

                                                                                aGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGgcg                                       <  1:137998/140‑1 (MQ=255)

                                                                                aGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGgcg                                       <  1:41051/140‑1 (MQ=255)

                                                                                       tatCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCgctggctg                                >  1:714864/1‑140 (MQ=255)

                                                                                            ggCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaaaa                           >  1:776239/1‑140 (MQ=255)

                                                                                            ggCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaaaa                           >  1:574376/1‑140 (MQ=255)

                                                                                            ggCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaaaa                           >  1:244068/1‑140 (MQ=255)

                                                                                            ggCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaa                             <  1:135821/138‑1 (MQ=255)

                                                                                            ggCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaa                             >  2:135821/1‑138 (MQ=255)

                                                                                                gAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATg                       >  1:535837/1‑140 (MQ=255)

                                                                                                gAATAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATg                       >  1:560738/1‑140 (MQ=255)

                                                                                                   tAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACg                    <  2:3446/140‑1 (MQ=255)

                                                                                                   tAAAAAGAAGGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACg                    <  1:690000/140‑1 (MQ=255)

                                                                                                           agGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTg            >  2:197362/1‑140 (MQ=255)

                                                                                                           agGTTTCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTg            <  2:535837/140‑1 (MQ=255)

                                                                                                                tCACAGAAAAAAATTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCaa       >  1:193270/1‑140 (MQ=255)

                                                                                                                     aaaaaaaaTTGCATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGc  <  2:193270/139‑1 (MQ=255)

GGAAACCACAAAAAGTGGTATGCAAACAACCGATCTGTCGCGTTTTTCAAAAAAATATGCACAACTACCAGGAACTTATCAGGTTGATATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAATTACATTTACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGC  >  NC_000913/3288963‑3289219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A