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 986,986 C→T 35.9% G409G (GGC→GGT)  ynfE → oxidoreductase subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE986,9860CT35.9% 61.0 / 51.1 89G409G (GGC→GGT) ynfEoxidoreductase subunit
Reads supporting (aligned to +/- strand):  ref base C (26/31);  new base T (18/14);  total (44/45)
Fisher's exact test for biased strand distribution p-value = 3.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAA  >  minE/986927‑987048
                                                           |                                                              
gcTATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGaa                                                       <  1:3379904/69‑1 (MQ=255)
gcTATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGaa                                                       <  1:407975/69‑1 (MQ=255)
gcTATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGaa                                                       <  1:1406157/69‑1 (MQ=255)
  tATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATc                                                     <  1:2241117/69‑1 (MQ=255)
  tATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATc                                                     <  1:804232/69‑1 (MQ=255)
  tATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATc                                                     <  1:1801342/69‑1 (MQ=255)
  tATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATc                                                     <  1:1679192/69‑1 (MQ=255)
  tATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATc                                                     <  1:2570679/69‑1 (MQ=255)
   aTTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCg                                                    <  1:1896199/69‑1 (MQ=255)
            ttACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtacc                                           <  1:2734395/69‑1 (MQ=255)
            ttACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtacc                                           <  1:110458/69‑1 (MQ=255)
            ttACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtacc                                           <  1:1163975/69‑1 (MQ=255)
            ttACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtacc                                           <  1:1350207/69‑1 (MQ=255)
            ttACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtacc                                           <  1:18531/69‑1 (MQ=255)
                     ttGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtaccattaccat                                   <  1:743770/68‑1 (MQ=255)
                     ttGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTAtaccattaccat                                   <  1:3241844/68‑1 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:583773/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:418539/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:2832417/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:1099203/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:2896218/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:2931289/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:3168994/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:593804/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:3121873/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:1793213/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:295204/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:2846442/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:2450912/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTAcaccattaccatcg                                 <  1:979811/68‑3 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:2673594/68‑1 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:335987/68‑1 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:2266277/68‑1 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:1642243/68‑1 (MQ=255)
                       gACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:1159801/68‑1 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                     >  1:923292/1‑69 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                     >  1:3052446/1‑69 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                     >  1:364525/1‑69 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                      >  1:2258896/1‑68 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                      >  1:3018501/1‑68 (MQ=255)
                                  tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                      >  1:3234892/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGATCGCTTGCCGGTg                   >  1:2361929/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:2971573/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:3158266/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:3354771/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:2694390/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:2280347/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:81731/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:2058107/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:1906135/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:880039/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:3397748/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:42134/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:1644527/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:156274/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:3434747/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:1459199/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:1411106/1‑68 (MQ=255)
                                     gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                   >  1:1071032/1‑68 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:40485/49‑1 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:3254277/49‑1 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:1466036/49‑1 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAg                                 <  1:765395/49‑1 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:788588/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:53656/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2774995/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:901616/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:988580/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:9916/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2976249/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2916048/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:379840/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2786974/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:105766/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:1065414/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2638183/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2537457/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2467098/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:1536816/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:2228971/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:1737155/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt             >  1:1733176/1‑69 (MQ=255)
                                          aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCCGGAt             >  1:2061500/1‑69 (MQ=255)
                                                     tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:1058476/69‑1 (MQ=255)
                                                     tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:169156/69‑1 (MQ=255)
                                                     tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:2377472/69‑1 (MQ=255)
                                                     tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:2402096/69‑1 (MQ=255)
                                                     tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:579026/69‑1 (MQ=255)
                                                      aGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa  <  1:2853657/68‑1 (MQ=255)
                                                           |                                                              
GCTATTGCTATGTTACCTATTTTGACGGGCAATGTCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAA  >  minE/986927‑987048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A