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
A1 F21 I0 R1	476	35.3	2812105	96.7%	2719305	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,547,129	G→A	87.8%	M137I (ATG→ATA)	fimE →	tyrosine recombinase/inversion of on/off regulator of fimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,547,129	0	G	A	87.8%	119.7 / 10.3	49	M137I (ATG→ATA)	fimE	tyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (32/11); total (34/15)
Fisher's exact test for biased strand distribution p-value = 6.24e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

AGGCCTATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCT  >  W3110S.gb/4547062‑4547197

agGCCTATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATAtt                                                                    >  1:438318/1‑70 (MQ=255)

 ggCCTATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATAtt                                                                    >  1:191892/1‑69 (MQ=255)

         gCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCt                                                          <  1:2035823/71‑1 (MQ=255)

         gCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCt                                                          >  1:541537/1‑71 (MQ=255)

         gCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCt                                                          >  1:60798/1‑71 (MQ=255)

              attCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCgg                                                     >  1:1821291/1‑71 (MQ=255)

              attCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCgg                                                     >  1:2460879/1‑71 (MQ=255)

              attCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCgg                                                     >  1:752898/1‑71 (MQ=255)

                 cgcgATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTa                                                  >  1:1494599/1‑71 (MQ=255)

                  gcgATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTa                                                  <  1:833895/70‑1 (MQ=255)

                    gATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGa                                               <  1:1270309/71‑1 (MQ=255)

                    gATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGa                                               <  1:896169/71‑1 (MQ=255)

                    gATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGa                                               <  1:440108/71‑1 (MQ=255)

                        ccGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGTGGTTATGAATTg                                           <  1:819527/71‑1 (MQ=255)

                        ccGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTg                                           >  1:1712632/1‑71 (MQ=255)

                        ccGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTg                                           <  1:2060907/71‑1 (MQ=255)

                             aTTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCg                                        >  1:1996310/1‑69 (MQ=255)

                              ttGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCgg                                       <  1:2295134/69‑1 (MQ=255)

                              ttGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAg                                     <  1:224756/71‑1 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTa                                                  >  1:2531568/1‑56 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTa                                                  >  1:1992873/1‑56 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGaa                                              >  1:1329044/1‑60 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGaa                                              >  1:2709274/1‑60 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGc                                    >  1:276708/1‑70 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCg                                   >  1:1250960/1‑71 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCg                                   >  1:2045952/1‑71 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCg                                   >  1:1367608/1‑71 (MQ=255)

                                gAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCg                                   >  1:665224/1‑71 (MQ=255)

                                 aaGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgt                                  <  1:1516343/71‑1 (MQ=255)

                                    cTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgtggt                               >  1:2383899/1‑71 (MQ=255)

                                    cTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgtggt                               >  1:1706947/1‑71 (MQ=255)

                                     tGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgtggtg                              >  1:1826137/1‑71 (MQ=255)

                                       gAACCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGc                                    <  1:1131504/63‑1 (MQ=255)

                                        aaCCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGc                                    <  1:1579380/62‑1 (MQ=255)

                                         aCCGTAACGCAGACTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgtggtg                              >  1:1128092/1‑67 (MQ=255)

                                            gTAACGCAGACTCATCCTCATATATTAAGGCATGc                                                           >  1:1519753/1‑35 (MQ=255)

                                            gTAACGCAGACTCATCCTCATATATTAAGGCATGc                                                           >  1:1523133/1‑35 (MQ=255)

                                                    gACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTaa               <  1:1975523/71‑1 (MQ=255)

                                                      cTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAAtt             >  1:1982868/1‑71 (MQ=255)

                                                      cTCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAAt              >  1:2274127/1‑70 (MQ=255)

                                                       tCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAAtt             >  1:437057/1‑70 (MQ=255)

                                                       tCATCCTCATATATTAAGGCATGCTTGCGGTTATg                                                <  1:1574665/35‑1 (MQ=255)

                                                       tCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCg                                        >  1:304173/1‑43 (MQ=255)

                                                       tCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGa                          >  1:2059281/1‑57 (MQ=255)

                                                       tCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAAtt             >  1:702208/1‑70 (MQ=255)

                                                       tCATCCTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAAtt             >  1:2736468/1‑70 (MQ=255)

                                                            cTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAt       >  1:1658145/1‑71 (MQ=255)

                                                            cTCATATATTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAt       <  1:2437046/71‑1 (MQ=255)

                                                               atatatTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGAtt      <  1:716081/69‑1 (MQ=255)

                                                                tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCgt                                  <  1:838600/40‑1 (MQ=255)

                                                                 atGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTAtct  >  1:1614298/1‑71 (MQ=255)

AGGCCTATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCT  >  W3110S.gb/4547062‑4547197

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A