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
A5 F17 I0 R2	162	60.6	4616657	98.5%	4547407	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	833,307	G→T	12.2%	T22T (ACC→ACA)	ybiA ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	833,307	0	G	T	12.2%	148.6 / 5.3	49	T22T (ACC→ACA)	ybiA	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (26/17); new base T (2/4); total (28/21)
Fisher's exact test for biased strand distribution p-value = 3.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

AGGCCAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTA  >  W3110S.gb/833238‑833374

aGGCCAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTgg                                                                    >  1:2074319/1‑71 (MQ=255)

     aGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTg                                                               <  1:1967055/71‑1 (MQ=255)

     aGGTTTTCCCGGCAACCTTGATGGGCCAGGCTGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGc                                                                 <  1:2493643/69‑1 (MQ=255)

       gTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTa                                                             <  1:2808872/71‑1 (MQ=255)

             ccGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAAtt                                                       <  1:4177052/71‑1 (MQ=255)

             ccGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAAtt                                                       <  1:2257202/71‑1 (MQ=255)

                tCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTg                                                                  >  1:3386749/1‑57 (MQ=255)

                  aaCCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatga                                                  >  1:1270620/1‑71 (MQ=255)

                    ccTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatgatg                                                >  1:2158303/1‑71 (MQ=255)

                     cTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTtgtg                                                                  >  1:1014305/1‑52 (MQ=255)

                       tGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTa                                                             >  1:4344001/1‑55 (MQ=255)

                         aTGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGgtgt                                            <  1:2232125/70‑1 (MQ=255)

                             gCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAAtt                                                       <  1:3651628/55‑1 (MQ=255)

                             gCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGc                                       <  1:1165476/71‑1 (MQ=255)

                              ccAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAAAAATTTATGATGGTGTCTTGCa                                      >  1:2971470/1‑71 (MQ=255)

                                  gctgcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCtt                                         >  1:776515/4‑64 (MQ=255)

                                   cggcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATg                                    <  1:907997/68‑1 (MQ=255)

                                    ggcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAAtt                                                       >  1:2340334/1‑48 (MQ=255)

                                     tcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATgg                                               <  1:1321071/54‑1 (MQ=255)

                                     gcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATgg                                               <  1:1950657/55‑1 (MQ=255)

                                       aaaGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTa                                                     >  1:2097557/1‑47 (MQ=255)

                                       aaaGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGAc                                  >  1:4352457/1‑66 (MQ=255)

                                       aaaGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGAc                                  >  1:2931168/1‑66 (MQ=255)

                                         aGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTgg                           <  1:4480171/71‑1 (MQ=255)

                                         aGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTgg                           <  1:734766/71‑1 (MQ=255)

                                           ttAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatg                                                   <  1:210182/45‑1 (MQ=255)

                                           ttAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     <  1:4501674/59‑1 (MQ=255)

                                           ttAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGAt                         >  1:1838265/1‑71 (MQ=255)

                                             aGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgtgt                              >  1:1818495/1‑64 (MQ=255)

                                                aaaaTCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCtt                     >  1:4250988/1‑70 (MQ=255)

                                                 aaaTCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTtg                   >  1:4105594/1‑71 (MQ=255)

                                                    tCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGc                >  1:361483/1‑71 (MQ=255)

                                                     cACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCt               >  1:3782934/1‑71 (MQ=255)

                                                      aCCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCt               >  1:4064326/1‑70 (MQ=255)

                                                       ccGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCg             <  1:4163272/71‑1 (MQ=255)

                                                        cGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgt                                <  1:2975251/51‑1 (MQ=255)

                                                         gTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     >  1:3784004/1‑45 (MQ=255)

                                                         gTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     >  1:2005432/1‑45 (MQ=255)

                                                         gTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGaa           >  1:2286159/1‑71 (MQ=255)

                                                          tAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAAc          >  1:3843201/1‑71 (MQ=255)

                                                           aGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCt                      <  1:1047901/58‑1 (MQ=255)

                                                           aGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACg         >  1:81661/1‑71 (MQ=255)

                                                            gTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACgg        >  1:181750/1‑71 (MQ=255)

                                                            gTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACg         <  1:433999/70‑1 (MQ=255)

                                                                tCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgtgt                              <  1:1444395/45‑1 (MQ=255)

                                                                 cGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAAc          >  1:3997771/1‑64 (MQ=255)

                                                                 cGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAAc          >  1:4573695/1‑64 (MQ=255)

                                                                 cGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCAt    >  1:3537747/1‑70 (MQ=255)

                                                                  gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCtt                     >  1:4047183/1‑52 (MQ=255)

                                                                  gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCtt                     >  1:4042064/1‑52 (MQ=255)

                                                                  gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTa  <  1:2639962/71‑1 (MQ=255)

AGGCCAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTA  >  W3110S.gb/833238‑833374

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