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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,324,790 T→C 25.7% Y185C (TAC→TGC)  phnI ← carbon‑phosphorus lyase complex subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,324,7900TC25.7% 54.7 / 21.5 35Y185C (TAC→TGC) phnIcarbon‑phosphorus lyase complex subunit
Reads supporting (aligned to +/- strand):  ref base T (16/10);  new base C (4/5);  total (20/15)
Fisher's exact test for biased strand distribution p-value = 4.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.10e-01

CCAGCGCCAGCAAATAGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACTTCGCCAGCCCCT  >  W3110S.gb/4324722‑4324859
                                                                    |                                                                     
ccagcgccagcAAATAGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCaa                                                                     <  1:3458429/71‑1 (MQ=255)
     gccagcAAATAGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACcg                                                                 >  1:2416004/1‑70 (MQ=255)
              tAGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCg                                                       >  1:1863517/1‑71 (MQ=255)
               aGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCgg                                                      >  1:3837029/1‑71 (MQ=255)
                    tcgtcgCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:1466353/1‑56 (MQ=255)
                    tcgtcgCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:2648223/1‑56 (MQ=255)
                    tcgtcgCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGAt                                                 >  1:3332954/1‑71 (MQ=255)
                     cgtcgCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATg                                                >  1:3550335/1‑71 (MQ=255)
                         gccgcGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCGGGTGATGTCa                                             <  1:3504081/70‑1 (MQ=255)
                         gccgcGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCGGGTGATGTCAt                                            <  1:2246403/71‑1 (MQ=255)
                         gccgcGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCGGGTGATGTCAt                                            <  1:3972899/71‑1 (MQ=255)
                             cgcATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTg                                                   >  1:571063/1‑60 (MQ=255)
                             cgcATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCGGGTGATGTCATCCgg                                        <  1:1521368/71‑1 (MQ=255)
                                aTCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCtg                                     <  1:2364810/71‑1 (MQ=255)
                                  cAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCtgtg                                   >  1:3800845/1‑71 (MQ=255)
                                  cAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCtgtg                                   >  1:4835021/1‑71 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:3378441/1‑41 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:4234985/1‑41 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:710787/1‑41 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcgg                                                                >  1:1917793/1‑41 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACcg                                                                 >  1:1921548/1‑40 (MQ=255)
                                   aaCTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTgc                                  >  1:744379/1‑71 (MQ=255)
                                     ctgctgCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGc                                                        >  1:179112/1‑47 (MQ=255)
                                     ctgctgCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTgcgc                                >  1:173200/1‑71 (MQ=255)
                                           cAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGGGATGTCATCCGGCTGTGCGCCGCTa                           <  1:4336560/70‑1 (MQ=255)
                                              aCGGGAGGAGCGTGAGCAGGGGCAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCct                       >  1:712406/1‑71 (MQ=255)
                                                gggAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATg                                                <  1:3042748/44‑1 (MQ=255)
                                                gggAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATg                                                <  1:3036975/44‑1 (MQ=255)
                                                gggAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATg                                                <  1:2214473/44‑1 (MQ=255)
                                                gggAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATg                                                <  1:3986956/44‑1 (MQ=255)
                                                   aggagCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCa                  <  1:4396471/71‑1 (MQ=255)
                                                       gCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACt              <  1:4228258/71‑1 (MQ=255)
                                                         gTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACTTc            <  1:3373501/71‑1 (MQ=255)
                                                            aGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACTTCGc          <  1:2010922/70‑1 (MQ=255)
                                                                   gTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACTTCGCCAGCCCCt  >  1:4995690/1‑71 (MQ=255)
                                                                    |                                                                     
CCAGCGCCAGCAAATAGCCTTCGTCGCCGCGCATCAACTGCTGCAAACGGGAGGAGCGTGAGCAGGGGTAAACCGGCGGCGTGCGGGTGATGTCATCCGGCTGTGCGCCGCTATCCTCTTCAAACTTCGCCAGCCCCT  >  W3110S.gb/4324722‑4324859

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