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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,780,496	G→A	34.9%	G66R (GGG→AGG)	yidK →	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,780,496	0	G	A	34.9%	73.8 / 62.6	67	G66R (GGG→AGG)	yidK	predicted transporter
Reads supporting (aligned to +/- strand): ref base G (26/17); new base A (11/12); total (37/30)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.39e-01

CCGGTTATTGCCGCTTCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACGCTGATCT  >  W3110S.gb/3780433‑3780562

ccGCTTATTGCCGCTTCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAg                                                               <  1:3347006/69‑1 (MQ=255)

 cGGTTATTGCCGCTTCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGGCGGCCTTTCCGGGCAgg                                                              <  1:2839291/69‑1 (MQ=255)

         gCCGCTTCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      <  1:2560473/69‑1 (MQ=255)

              ttCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCgg                                                 <  1:853432/69‑1 (MQ=255)

              ttCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGGCGGCCTTTCCGGGCAGGCCTACAAAAGCgg                                                 <  1:1487104/69‑1 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      <  1:930633/61‑1 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:928190/1‑61 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:1247757/1‑61 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      <  1:1269758/61‑1 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:1378067/1‑61 (MQ=255)

                 gTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:2779756/1‑61 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:2558002/1‑58 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:541694/1‑58 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:3442174/1‑58 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:1500228/1‑58 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaa                                                       >  1:1709796/1‑57 (MQ=255)

                    aaTGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTc                                           <  1:3498308/69‑1 (MQ=255)

                      tGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCAt                                              <  1:3350054/64‑1 (MQ=255)

                      tGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCAt                                              <  1:2440423/64‑1 (MQ=255)

                      tGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCAt                                              <  1:1135449/64‑1 (MQ=255)

                      tGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGt                                            >  1:1433820/1‑66 (MQ=255)

                      tGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCg                                          >  1:828308/1‑68 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCGTTTCCGGGCAGGCCTACAAAAGCGGCAt                                              <  1:320747/63‑1 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGt                                        <  1:23944/69‑1 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGt                                        <  1:2611543/69‑1 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGt                                        <  1:2432980/69‑1 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGt                                        <  1:1734899/69‑1 (MQ=255)

                       gCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGt                                        <  1:841384/69‑1 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:230488/1‑54 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:1584552/1‑54 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACaaa                                                      >  1:1580400/1‑54 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAg                                                    >  1:2614278/1‑56 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTc                                           >  1:3653661/1‑65 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTg                                       >  1:233362/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTg                                       >  1:2388034/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTg                                       >  1:2110828/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTg                                       >  1:1755263/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTg                                       >  1:2671669/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGCGCAGGCCTACAAAAGCGGCAAGTCGCTg                                       >  1:2331771/1‑69 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCAGGc                                                                 >  1:1913876/1‑43 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTACCg                                                                    >  1:3404247/1‑40 (MQ=255)

                        cTAACCAACCTTTCCACGGAACAACTGGTCGGCATTTCCAGGc                                                                 >  1:2857540/1‑43 (MQ=38)

                             caaccTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATggg                                  <  1:572694/69‑1 (MQ=255)

                             caaccTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATggg                                  <  1:3173190/69‑1 (MQ=255)

                             caaccTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATggg                                  <  1:3271675/69‑1 (MQ=255)

                                ccTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCgg                                                 <  1:72816/51‑1 (MQ=255)

                                 cTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTg                               >  1:3526805/1‑68 (MQ=255)

                                 cTTTCCACGGAACAACTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTg                               >  1:2190109/1‑68 (MQ=255)

                                 cTTTCCACGGAACAACTGGTCGGCCTTCCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTg                               >  1:1023895/1‑68 (MQ=255)

                                   ttCCACGGAACAACTGGTCGGCCTTTCCTGTCAGGCCTACTAAAGCgg                                                 <  1:1154200/48‑1 (MQ=38)

                                    tCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGaa                           >  1:2081499/1‑69 (MQ=255)

                                        cGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATg                                    >  1:1050418/1‑56 (MQ=255)

                                        cGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATg                                    <  1:3216170/56‑1 (MQ=255)

                                        cGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATg                                    >  1:1887064/1‑56 (MQ=255)

                                        cGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATg                                    <  1:2683490/56‑1 (MQ=255)

                                               tcTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGc                >  1:870497/2‑69 (MQ=255)

                                               acTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGc                >  1:719073/1‑69 (MQ=255)

                                               acTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGc                >  1:2670700/1‑69 (MQ=255)

                                               acTGGTCGGCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGc                >  1:1213712/1‑69 (MQ=255)

                                                cTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCg               >  1:1779066/1‑69 (MQ=255)

                                                  ggTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGt             >  1:3138018/1‑69 (MQ=255)

                                                  ggTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGt             >  1:180827/1‑69 (MQ=255)

                                                     cGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGa           <  1:1407273/68‑1 (MQ=255)

                                                     cGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGa           <  1:2877961/68‑1 (MQ=255)

                                                     cGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGa           <  1:806256/68‑1 (MQ=255)

                                                      ggCCTTTCCAGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACg         <  1:1808010/69‑1 (MQ=255)

                                                              cGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACGCTGATCt  <  1:2709467/68‑1 (MQ=255)

                                                              cGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACGCTGATCt  <  1:1396699/68‑1 (MQ=255)

                                                               gggCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACGCTGATCt  <  1:255780/67‑1 (MQ=255)

CCGGTTATTGCCGCTTCGTTAATGCTAACCAACCTTTCCACGGAACAACTGGTCGGCCTTTCCGGGCAGGCCTACAAAAGCGGCATGTCGGTGATGGGCTGGGAAGTGACTTCAGCGGTGACGCTGATCT  >  W3110S.gb/3780433‑3780562

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