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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,463,502 C→T P299L (CCG→CTG)  paaJ → predicted beta‑ketoadipyl CoA thiolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,463,5020CT95.0% 53.3 / ‑4.2 20P299L (CCG→CTG) paaJpredicted beta‑ketoadipyl CoA thiolase
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (5/14);  total (5/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CGGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGTGATTGA  >  W3110S.gb/1463441‑1463568
                                                             |                                                                  
cgGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGc                                                           <  1:815751/71‑1 (MQ=255)
                ccATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGt                                               <  1:129017/67‑1 (MQ=255)
                ccATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGt                                               <  1:1730256/67‑1 (MQ=255)
                ccATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGt                                               <  1:34770/67‑1 (MQ=255)
                          cgccgGGGTGGAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGt                                               <  1:864094/57‑1 (MQ=255)
                                    gAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTAt                       >  1:1248012/1‑71 (MQ=255)
                                    gAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTAt                       >  1:3262260/1‑71 (MQ=255)
                                    gAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTAt                       >  1:2549477/1‑71 (MQ=255)
                                    gAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTAt                       >  1:2192191/1‑71 (MQ=255)
                                    gAACCGCGCCTGATGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTAt                       >  1:1340714/1‑71 (MQ=255)
                                              ttaTGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAAcgcg                                    <  1:2910559/46‑1 (MQ=39)
                                                 tGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:2838807/71‑1 (MQ=255)
                                                 tGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:2077626/71‑1 (MQ=255)
                                                 tGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:3930032/71‑1 (MQ=255)
                                                 tGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:488518/71‑1 (MQ=255)
                                                 tGGGGCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:1120887/71‑1 (MQ=255)
                                                  ggggCTTGGTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGAc          <  1:640488/70‑1 (MQ=255)
                                                         ggTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGTACGTGATtg   <  1:3148688/70‑1 (MQ=255)
                                                          gTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGTGATtga  <  1:3492950/70‑1 (MQ=255)
                                                          gTCTGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGTGATtga  <  1:3612779/70‑1 (MQ=255)
                                                             |                                                                  
CGGGCGCGTATCGTAGCCATGGCAACCGCCGGGGTGGAACCGCGCCTGATGGGGCTTGGTCCGGTGCCTGCAACTCGCCGGGTGCTGGAACGCGCAGGGCTGAGTATTCACGATATGGACGTGATTGA  >  W3110S.gb/1463441‑1463568

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