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
A34 F6 I0 R1 1504 343.2 14897860 96.8% 14421128 147.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,825,970 2 bp→CT 100% coding (742‑743/1422 nt) PP_1624 → group II intron‑encoding maturase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,825,9700TC93.8% 44.6 / ‑3.7 16S248M (TCG→CTG) PP_1624group II intron‑encoding maturase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (10/5);  total (10/6)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*NC_0029471,825,9710CT93.8% 45.9 / ‑3.9 16S248M (TCG→CTG) PP_1624group II intron‑encoding maturase
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (10/5);  total (10/6)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGG  >  NC_002947/1825937‑1826096
                                 ||                                                                                                                             
cGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTTTCGCCGTtggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttatctttgacccggcgctcgatacaggccatcaggatgtcgtg            <  1:2907920‑M1/150‑111 (MQ=255)
      gaggGGACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttga                                              <  1:2770602‑M1/109‑77 (MQ=255)
      gaggGGACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttga                                              >  2:2770602‑M1/1‑33 (MQ=255)
       aggGGACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgaccc    >  1:3593499‑M1/1‑32 (MQ=255)
       aggGGACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgaccc    >  1:3762770‑M1/1‑32 (MQ=255)
       aggGGACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgaccc    >  1:3762943‑M1/1‑32 (MQ=255)
        ggggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccg   >  1:2821545‑M1/1‑31 (MQ=255)
        ggggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccg   >  2:5045986‑M1/1‑31 (MQ=255)
         gggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccga  <  1:5045986‑M1/150‑121 (MQ=255)
         gggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccga  >  2:3880570‑M1/1‑30 (MQ=255)
         gggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgat                                             <  1:5243764‑M1/107‑78 (MQ=255)
         gggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgat                                             >  2:5243764‑M1/1‑30 (MQ=255)
           gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgatt         >  1:6157699‑M1/1‑28 (MQ=255)
           gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgatt         <  2:6157699‑M1/141‑114 (MQ=255)
           gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcga                                  <  1:5075429‑M1/116‑89 (MQ=255)
           gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcga                                  >  2:5075429‑M1/1‑28 (MQ=255)
                                 ||                                                                                                                             
CGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGG  >  NC_002947/1825937‑1826096

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A