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 900,737 T→C 36.0% S194S (AGT→AGC)  ycjM → predicted glucosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE900,7370TC36.0% 59.7 / 59.8 97S194S (AGT→AGC) ycjMpredicted glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (49/13);  new base C (31/4);  total (80/17)
Fisher's exact test for biased strand distribution p-value = 2.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

Only 100 of 118 total aligned reads displayed.

ACCGTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGAAGTGTTGCTGGCGATGGTGGAT  >  minE/900674‑900794
                                                               |                                                         
aCCGTTATTAACGCCATTCCAGATTCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:3286597/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1619616/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:2071873/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:3424166/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:3344350/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:500922/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:2437794/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:2504765/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:686581/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:2867505/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:854243/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1301664/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:2706836/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1283986/69‑1 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACg                                                       >  1:259106/1‑68 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACg                                                       >  1:1949686/1‑68 (MQ=255)
aCCGTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACg                                                       >  1:1331254/1‑68 (MQ=255)
aCCGTTATTAACGCCATTCCAGAT‑‑GCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGAt                                                     >  1:526271/1‑68 (MQ=255)
 ccGTTATTAACGCCATTCCAGATTCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1399192/68‑1 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTATTGACGATCa                                                   >  1:2408430/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:2463628/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:1589496/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:659365/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:2973594/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:2093027/1‑69 (MQ=255)
   gTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCa                                                   >  1:2052544/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1718519/60‑1 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:2829154/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:3250941/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:330975/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:2135918/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:2884984/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:62959/1‑69 (MQ=255)
         aaCGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGa                                             >  1:625113/1‑69 (MQ=255)
             ccATTCCAGATGCGCGATCATTCAACGCGCCATTTATGTACCACCTTTAGTGACGATCAAATTGACCTg                                         <  1:770837/69‑1 (MQ=255)
             ccATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTg                                         <  1:358193/69‑1 (MQ=255)
             ccATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTg                                         <  1:1999516/69‑1 (MQ=255)
             ccATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTg                                         <  1:2983192/69‑1 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:458881/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:899037/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:865417/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2891939/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:1079317/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:1127841/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:321879/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:322179/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:1520493/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2467332/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:1674123/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:609469/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:1806082/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:330581/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2374294/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:506013/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:48015/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:3374321/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2242801/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:3411901/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2189209/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:2184543/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGATCa                                                   >  1:217509/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGAAGATCa                                                   >  1:2494562/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAATGCGCCATTTATGGACAACCTTTAGCGACGATCa                                                   >  1:2326041/1‑54 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACTATCAAATTGACCTGAAtt                                     >  1:1007462/1‑68 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:420653/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:2020836/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:2092595/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:1909634/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:1810193/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:606658/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:1670444/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:151115/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:2950390/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:2749640/1‑69 (MQ=255)
                  ccAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTa                                    >  1:2787976/1‑69 (MQ=255)
                  ccAGATGAGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGa                                                         >  1:2721445/1‑48 (MQ=255)
                  ccACATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGCGACGAta                                                    >  1:2569513/1‑52 (MQ=255)
                     gATGCGCGATCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:1901337/48‑1 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTg                                                          >  1:2734518/1‑42 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:1874460/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:1495363/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:1411426/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:1013490/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:2053553/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:2449776/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:2387443/1‑69 (MQ=255)
                       tGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTa                               >  1:2206332/1‑69 (MQ=255)
                             aTCATTCAATGCGCCATTTATGGACCACCTTTAGcgacga                                                      <  1:3303070/40‑1 (MQ=38)
                              tCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGa                        <  1:2259481/69‑1 (MQ=255)
                              tCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGa                        <  1:2902777/69‑1 (MQ=255)
                              tCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGa                        <  1:2737136/69‑1 (MQ=255)
                               cATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGaa                       >  1:435948/1‑69 (MQ=255)
                               cATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGaa                       >  1:1091660/1‑69 (MQ=255)
                               cATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGa                        <  1:2626269/68‑1 (MQ=255)
                                     atgcgcCATTTATGGACCACCTTTAGCGACGATCAAATTGACCTCAATTAc                                   <  1:1698864/49‑1 (MQ=255)
                                     atgcgcCATTTATGGACCACCTTTAGCGACGATCAAATTGACCTCAATTAc                                   <  1:140783/49‑1 (MQ=255)
                                     atgcgcCATTTATGGACCACCTTTAGCGACGATCAAATTGACCTCAATTAc                                   <  1:2805063/49‑1 (MQ=255)
                                          ccATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGAAGTGTTGCTGGc            <  1:1026012/69‑1 (MQ=255)
                                          ccATTTATGGACCACCTTTAGCGACGATCAAATTGACCTCAATTAc                                   <  1:2335725/46‑1 (MQ=39)
                                                     ccaccTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGAAGTGTTGCTGGCGATGGTGGAt  <  1:861971/68‑1 (MQ=255)
                                                               |                                                         
ACCGTTATTAACGCCATTCCAGATGCGCGATCATTCAACGCGCCATTTATGGACCACCTTTAGTGACGATCAAATTGACCTGAATTACCGTAGCCCTGAAGTGTTGCTGGCGATGGTGGAT  >  minE/900674‑900794

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