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
A2 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	899,197	C→T	20.9%	P78L (CCT→CTT)	pspC →	transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	899,197	0	C	T	20.9%	144.1 / 33.2	67	P78L (CCT→CTT)	pspC	transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (28/25); new base T (6/8); total (34/33)
Fisher's exact test for biased strand distribution p-value = 5.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.85e-01

CATCATTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGTTTACGCGA  >  minE/899135‑899263

catcatTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCcagca                                                            <  1:868760/71‑1 (MQ=255)

 atcatTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCcagcag                                                           >  1:878493/1‑71 (MQ=255)

 atcatTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCcagcag                                                           >  1:2082768/1‑71 (MQ=255)

 atcatTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCcagcag                                                           >  1:3831498/1‑71 (MQ=255)

     ttttGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGaa                                                       >  1:840064/1‑71 (MQ=255)

     ttttGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGaa                                                       >  1:2600404/1‑71 (MQ=255)

     ttttGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGa                                                        >  1:622752/1‑70 (MQ=255)

         gTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   >  1:2594491/1‑71 (MQ=255)

          tCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   <  1:3802662/70‑1 (MQ=255)

          tCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   <  1:3268537/70‑1 (MQ=255)

          tCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   <  1:3462040/70‑1 (MQ=255)

          tCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   <  1:48359/70‑1 (MQ=255)

          tCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGc                                                   <  1:795556/70‑1 (MQ=255)

              ttGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:671132/1‑71 (MQ=255)

              ttGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:2434604/1‑71 (MQ=255)

               tGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:3608505/1‑70 (MQ=255)

               tGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:4091163/1‑70 (MQ=255)

               tGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:3010430/1‑70 (MQ=255)

               tGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGAt                                              >  1:2476381/1‑70 (MQ=255)

                gcgcTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATg                                             <  1:1135703/70‑1 (MQ=255)

                gcgcTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATg                                             <  1:3135335/70‑1 (MQ=255)

                        tCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGAcc                                    <  1:3147277/71‑1 (MQ=255)

                        tCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGAcc                                    <  1:701480/71‑1 (MQ=255)

                           aaTGCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTg                                 <  1:2423906/71‑1 (MQ=255)

                            aTGCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTc                                                                 <  1:816783/38‑1 (MQ=255)

                            aTGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTg                                 >  1:3124852/1‑70 (MQ=255)

                              gCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCCagcagc                                                          >  1:1023029/1‑43 (MQ=255)

                              gCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCCagcagc                                                          >  1:1716050/1‑43 (MQ=255)

                              gCCGGACAACATGGCCTTTGGTGAGCAGCTACTTTCCagcagc                                                          >  1:299353/1‑43 (MQ=255)

                              gCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               >  1:1878375/1‑70 (MQ=255)

                                cGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTg                            <  1:1804443/71‑1 (MQ=255)

                                cGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTg                            <  1:1999649/71‑1 (MQ=255)

                                     aacaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTggcggc                       <  1:2900478/71‑1 (MQ=255)

                                     aacaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTggcggc                       <  1:1141817/71‑1 (MQ=255)

                                      acaTGGCCTTTGGTGAGCAGCTACCTTCCTGCAGCg                                                         <  1:5341/36‑1 (MQ=255)

                                      acaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCg                                                         <  1:2183758/36‑1 (MQ=255)

                                      acaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCg                                                         <  1:3820856/36‑1 (MQ=255)

                                      acaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTggcggc                       <  1:225233/70‑1 (MQ=255)

                                      acaTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCa                      <  1:2809301/71‑1 (MQ=255)

                                        aTGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAg                    >  1:3048024/1‑71 (MQ=255)

                                              tttGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGa                                            <  1:2965222/41‑1 (MQ=255)

                                               ttGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               >  1:3785513/1‑53 (MQ=255)

                                               ttGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               >  1:1239249/1‑53 (MQ=255)

                                               ttGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               >  1:1872330/1‑53 (MQ=255)

                                               ttGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               >  1:520308/1‑53 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGa                                               >  1:3596979/1‑36 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGa                                               >  1:1228242/1‑36 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGa                                               >  1:1658045/1‑36 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGa                                               >  1:3601561/1‑36 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGa                                               >  1:2053161/1‑36 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAAcgc            >  1:725652/1‑71 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAAcgc            >  1:283066/1‑71 (MQ=255)

                                                tGGTGAGCAGCTACCTTCCAGCAGCGAATT‑CTGGa                                               >  1:232843/1‑35 (MQ=38)

                                                 gttGAGAAGATACCTTCCAGCAGCGAATTGCTGGATGAAGTCGAcc                                    <  1:2053513/44‑1 (MQ=255)

                                                 ggTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAAcgc            <  1:3272893/70‑1 (MQ=255)

                                                   tGAGCAGCTACTTTCCAGCAGCGAATTGCTGGATGAAGTCg                                       <  1:2075125/41‑1 (MQ=255)

                                                   tGAGCAGCTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGtt         <  1:4085645/71‑1 (MQ=255)

                                                   tGAGCAGCTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGtt         <  1:3034498/71‑1 (MQ=255)

                                                   tGAGCAGCTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGtt         <  1:2244145/71‑1 (MQ=255)

                                                   tGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGtt         <  1:1725743/71‑1 (MQ=255)

                                                       cagcTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGTTTAcg     >  1:2202182/1‑71 (MQ=255)

                                                          cTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGaa                               <  1:1201985/42‑1 (MQ=255)

                                                          cTACTTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGTTTACGCga  <  1:3609334/71‑1 (MQ=255)

                                                          cTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTTAACTGGCGGCAAGTGAAACGCGTTTACGCga  <  1:3851084/71‑1 (MQ=255)

                                                          cTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGTTTACGCga  <  1:2613547/71‑1 (MQ=255)

                                                            aCCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAAc                              >  1:2425275/1‑41 (MQ=255)

                                                            aCCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACt                             >  1:2239496/1‑42 (MQ=255)

CATCATTTTGTCATTTGCGCTTGATCCAATGCCGGACAACATGGCCTTTGGTGAGCAGCTACCTTCCAGCAGCGAATTGCTGGATGAAGTCGACCGTGAACTGGCGGCAAGTGAAACGCGTTTACGCGA  >  minE/899135‑899263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A