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 F28 I1 R1	128	54.7	1845674	99.3%	1832754	139.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,186,103	G→C	intergenic (+8/‑84)	yqiG → / → insC‑5	putative outer membrane usher protein YqiG/IS2 insertion element repressor InsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,186,103	0	G	C	100.0%	130.6 / NA	37	intergenic (+8/‑84)	yqiG/insC‑5	putative outer membrane usher protein YqiG/IS2 insertion element repressor InsA
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (17/20); total (17/20)

TTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCA  >  NC_000913/3185971‑3186229

tttGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTg                                                                                                                         >  1:772902/1‑140 (MQ=255)

        ggTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCa                                                                                                                 <  2:24193/140‑1 (MQ=255)

        ggTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCa                                                                                                                 <  1:726041/140‑1 (MQ=255)

         gTTCGCCCGGCCACATCATTAACTGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAg                                                                                                                <  2:791324/140‑1 (MQ=255)

                                  aTTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTg                                                                                       >  1:718623/1‑140 (MQ=255)

                                    tcaTGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAt                                                                                     <  2:853820/138‑1 (MQ=255)

                                            aGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGa                                                                                      <  2:859583/131‑1 (MQ=255)

                                            aGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGa                                                                                      >  1:859583/1‑131 (MQ=255)

                                            aGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTaa                                                                             >  1:912483/1‑140 (MQ=255)

                                            aGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTaa                                                                             >  1:910652/1‑140 (MQ=255)

                                                gATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt                                                                         >  1:591254/1‑140 (MQ=255)

                                                gATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt                                                                         <  2:718623/140‑1 (MQ=255)

                                                 aTCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt                                                                               >  1:673954/1‑133 (MQ=255)

                                                 aTCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt                                                                               <  2:673954/133‑1 (MQ=255)

                                                  tCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAg                                                                       >  1:308293/1‑140 (MQ=255)

                                                      aTGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt                                                                         <  1:837336/134‑1 (MQ=255)

                                                      aTGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt                                                                         >  2:837336/1‑134 (MQ=255)

                                                      aTGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGtttt                                                                   >  1:635644/1‑140 (MQ=255)

                                                        gTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTa                                                                 >  2:688079/1‑140 (MQ=255)

                                                           taAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAc                                                              >  2:585499/1‑140 (MQ=255)

                                                           taAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAc                                                              <  1:358188/140‑1 (MQ=255)

                                                           taAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAc                                                              <  2:164679/140‑1 (MQ=255)

                                                           taAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAc                                                              >  1:887979/1‑140 (MQ=255)

                                                            aaaaaaTTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACt                                                             <  2:398390/140‑1 (MQ=255)

                                                               aaattaaaattaACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGt                                                          <  2:591254/140‑1 (MQ=255)

                                                                   taaaattaaCCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCAtt                                                      >  1:374455/1‑140 (MQ=255)

                                                                    aaaattaaCCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                     <  2:912483/140‑1 (MQ=255)

                                                                      aattaaCCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGga                                                   <  1:585499/140‑1 (MQ=255)

                                                                           aCCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACa                                              <  2:887979/140‑1 (MQ=255)

                                                                            ccACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCGCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAg                                             <  1:379978/140‑1 (MQ=255)

                                                                             cacaATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAga                                            <  1:673936/140‑1 (MQ=255)

                                                                                             aTTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAgg                            >  2:126304/1‑140 (MQ=255)

                                                                                                     tatttattGTTCATTATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGgaga                    <  1:688079/140‑1 (MQ=255)

                                                                                                                   tATCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGt      >  2:241943/1‑140 (MQ=37)

                                                                                                                     tCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAc    <  2:541640/140‑1 (MQ=25)

                                                                                                                     tCCGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAc    >  1:691457/1‑140 (MQ=25)

                                                                                                                       cGTTATTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACca  <  2:308293/140‑1 (MQ=18)

TTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCA  >  NC_000913/3185971‑3186229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A