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 F28 I1 R2	328	63.0	4687567	98.0%	4593815	65.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,074,141	C→T	Q156* (CAG→TAG)	flu →	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,074,141	0	C	T	100.0%	87.9 / NA	30	Q156* (CAG→TAG)	flu	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/13); total (17/13)

TTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCA  >  W3110S.gb/2074073‑2074207

ttATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAg                                                                  >  1:3533079/1‑71 (MQ=255)

 tATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAg                                                                  <  1:1991576/70‑1 (MQ=255)

      gTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATg                                                            <  1:420706/71‑1 (MQ=255)

        gCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCa                                                          >  1:1369295/1‑71 (MQ=255)

        gCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCa                                                          >  1:1544303/1‑71 (MQ=255)

        gCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCa                                                          >  1:2383173/1‑71 (MQ=255)

         ccGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCAt                                                         >  1:3752333/1‑71 (MQ=255)

         ccGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCAt                                                         >  1:3108592/1‑71 (MQ=255)

         ccGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCAt                                                         >  1:3012752/1‑71 (MQ=255)

                        gCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTgg                                                               >  1:3723825/1‑50 (MQ=255)

                             cAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAg                                      >  1:3046698/1‑70 (MQ=255)

                              aGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGa                                    <  1:2828939/71‑1 (MQ=255)

                                ggACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATg                                                            <  1:2213338/45‑1 (MQ=255)

                                ggACGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATg                                                            <  1:3016800/45‑1 (MQ=255)

                                  aCGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAcca                                >  1:1326023/1‑70 (MQ=255)

                                  aCGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAcca                                >  1:141404/1‑70 (MQ=255)

                                   cGGGCTGTGAACACCACGCTGAATGTTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAccat                               <  1:1161563/71‑3 (MQ=255)

                                   cGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAccat                               <  1:1747532/71‑3 (MQ=255)

                                   cGGGCTGTGAACACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAccat                               <  1:4020616/71‑3 (MQ=255)

                                            aaCACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa                      <  1:2607573/71‑1 (MQ=255)

                                            aaCACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa                      <  1:3880816/71‑1 (MQ=255)

                                             acacCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCAtt                           <  1:722630/65‑1 (MQ=255)

                                                  acGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAggg                >  1:3353554/1‑71 (MQ=255)

                                                  acGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAggg                >  1:4365567/1‑71 (MQ=255)

                                                       gAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAAccat                               <  1:780643/51‑3 (MQ=255)

                                                            gtggCGAATAGTGTATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc      >  1:1464507/1‑71 (MQ=255)

                                                            gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc      >  1:2754740/1‑71 (MQ=255)

                                                            gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc      >  1:238156/1‑71 (MQ=255)

                                                            gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc      >  1:941190/1‑71 (MQ=255)

                                                                cGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCa  <  1:2512666/71‑1 (MQ=255)

TTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCA  >  W3110S.gb/2074073‑2074207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A