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 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,238,998	G→A	32.7%	T411T (ACC→ACT)	zwf ←	glucose‑6‑phosphate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,238,998	0	G	A	32.7%	54.8 / 32.9	67	T411T (ACC→ACT)	zwf	glucose‑6‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand): ref base G (29/16); new base A (8/14); total (37/30)
Fisher's exact test for biased strand distribution p-value = 3.85e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

AAACGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAGGAACTT  >  minE/1238960‑1239065

aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                                       <  1:371882/69‑1 (MQ=255)

aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                                       <  1:2789143/69‑1 (MQ=255)

aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                                       <  1:671885/69‑1 (MQ=255)

aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                                       <  1:3296989/69‑1 (MQ=255)

aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                                       <  1:836692/69‑1 (MQ=255)

    gTTCATAGGCATGTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:812224/54‑1 (MQ=255)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:2194741/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:59431/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:1957294/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:1889050/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:1755411/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:824563/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:1735233/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:2409029/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:3106221/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:2942287/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:950885/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:2949980/54‑1 (MQ=38)

    gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                                  <  1:3099524/54‑1 (MQ=38)

          aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             <  1:204245/69‑1 (MQ=255)

          aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             <  1:2538543/69‑1 (MQ=255)

          aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             <  1:27087/69‑1 (MQ=255)

          aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             <  1:355574/69‑1 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt                            >  1:989889/1‑69 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt                            >  1:868844/1‑69 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt                            >  1:3312071/1‑69 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt                            >  1:1540686/1‑69 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt                            >  1:649619/1‑69 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             >  1:1325732/1‑68 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             >  1:1348102/1‑68 (MQ=255)

           ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                             <  1:2542920/68‑1 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:1285861/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:2520459/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:2377604/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:3111647/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:2207402/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:843067/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:1865542/1‑57 (MQ=255)

              aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                                     >  1:1893416/1‑57 (MQ=255)

                 cGCCAGATGCGTCTGATTAAAGGTTTCTGAATGGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGttt                      >  1:94693/1‑69 (MQ=255)

                 cGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGttt                      >  1:1591124/1‑69 (MQ=255)

                   ccAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg                     <  1:2395119/68‑1 (MQ=255)

                   ccAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg                     <  1:1311795/68‑1 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATg                         >  1:1132857/1‑59 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTc                >  1:2243406/1‑68 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:205552/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:995857/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1069445/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:129815/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1398297/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:8416/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1620593/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1746497/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1788289/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:1831004/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:309435/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:2069771/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:2077209/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:2079017/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:3312323/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:228603/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:2350062/1‑69 (MQ=255)

                        tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa               >  1:2767244/1‑69 (MQ=255)

                            tCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg                     <  1:3014434/59‑1 (MQ=255)

                                  tAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAgg       <  1:344865/67‑1 (MQ=255)

                                  tAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAgg       <  1:1608590/67‑1 (MQ=255)

                                  tAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAgg       <  1:3110096/67‑1 (MQ=255)

                                      ggTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAGGAACtt  <  1:658135/68‑1 (MQ=255)

                                      ggTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAGGAACtt  <  1:1378899/68‑1 (MQ=255)

AAACGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCAAGGCCAGGAACTT  >  minE/1238960‑1239065

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