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 1,238,989 C→T 29.6% Q414Q (CAG→CAA)  zwf ← glucose‑6‑phosphate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,238,9890CT29.6% 74.9 / 31.8 74Q414Q (CAG→CAA) zwfglucose‑6‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base C (33/19);  new base T (8/14);  total (41/33)
Fisher's exact test for biased strand distribution p-value = 4.21e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.26e-01

CAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCA  >  minE/1238922‑1239052
                                                                   |                                                               
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                >  1:2483829/1‑69 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                >  1:2485864/1‑69 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:561870/69‑1 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:2548941/69‑1 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:2668771/69‑1 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:3041113/69‑1 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                >  1:1837413/1‑69 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:895784/69‑1 (MQ=255)
cAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                >  1:2824773/1‑69 (MQ=255)
            gAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCt                                                                <  1:934418/57‑1 (MQ=255)
                                      aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                          <  1:371882/69‑1 (MQ=255)
                                      aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                          <  1:671885/69‑1 (MQ=255)
                                      aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                          <  1:836692/69‑1 (MQ=255)
                                      aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                          <  1:2789143/69‑1 (MQ=255)
                                      aaaCGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTg                          <  1:3296989/69‑1 (MQ=255)
                                          gTTCATAGGCATGTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:812224/54‑1 (MQ=255)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:1735233/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:1889050/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:2409029/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:1957294/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:3106221/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:2949980/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:824563/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:1755411/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:2942287/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:2194741/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:3099524/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:59431/54‑1 (MQ=38)
                                          gTTCATAGGCATCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGAt                                     <  1:950885/54‑1 (MQ=38)
                                                aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                <  1:355574/69‑1 (MQ=255)
                                                aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                <  1:2538543/69‑1 (MQ=255)
                                                aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                <  1:204245/69‑1 (MQ=255)
                                                aGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                <  1:27087/69‑1 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt               >  1:3312071/1‑69 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt               >  1:989889/1‑69 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt               >  1:649619/1‑69 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt               >  1:1540686/1‑69 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGtt               >  1:868844/1‑69 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                <  1:2542920/68‑1 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                >  1:1325732/1‑68 (MQ=255)
                                                 ggCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGt                >  1:1348102/1‑68 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:2520459/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:3111647/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:1285861/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:843067/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:1865542/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:1893416/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:2207402/1‑57 (MQ=255)
                                                    aTCTGCCAGATGCGTTTGATTAAAAGTTTCTGAATAGCTCAGATCCAGCTTGGTGAt                        >  1:2377604/1‑57 (MQ=255)
                                                       cGCCAGATGCGTCTGATTAAAGGTTTCTGAATGGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGttt         >  1:94693/1‑69 (MQ=255)
                                                       cGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGttt         >  1:1591124/1‑69 (MQ=255)
                                                         ccAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg        <  1:1311795/68‑1 (MQ=255)
                                                         ccAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg        <  1:2395119/68‑1 (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  >  1:1620593/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:1746497/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:1788289/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:1831004/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:8416/1‑69 (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  >  1:228603/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:2350062/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:2767244/1‑69 (MQ=255)
                                                              tGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCa  >  1:3312323/1‑69 (MQ=255)
                                                                  tCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTtg        <  1:3014434/59‑1 (MQ=255)
                                                                   |                                                               
CAAACAGTGCCTGAATACCACGCATGGTTTCCAGCAGCAAACGTTCATAGGCATCCGCCAGATGCGTCTGATTAAAGGTTTCTGAATAGCTCAGATCCAGCTTGGTGATTTGCAGGTTATGTTTGTGGTCA  >  minE/1238922‑1239052

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