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
A3 F48 I1 R1 58 71.3 3054194 98.3% 3002272 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 1,499,480 2 bp→AC intergenic (+57/‑106) trpS → / → zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,499,4800CA80.0% 20.4 / ‑4.9 10intergenic (+57/‑107)trpS/zapEtryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (0/2);  new base A (6/2);  total (6/4)
Fisher's exact test for biased strand distribution p-value = 1.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*NC_002947_CJ‑RC1,499,4810AC90.0% 24.0 / ‑5.7 10intergenic (+58/‑106)trpS/zapEtryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (6/3);  total (6/4)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGT‑GTT‑TCG‑GG‑CA‑CG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAG  >  NC_002947_CJ‑RC/1499354‑1499611
                                                                                                                              ||                                                                                                                                         
cGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑Gttcgcg                                                                                                                     <  2:10879/148‑5 (MQ=255)
                                                           agccgGACTGCGGCGGCCACCGGGGGGGCGGGGGCGTCCCCCCTAAACCGGCGCGGCGGTGC‑TGGCCCCGGGCTTTGCCGGTGGGC‑GCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGcc                                                      <  6:337651/149‑1 (MQ=255)
                                                                                          gggCGCGCCCGCCAACCTGCCCCCG‑GGTGCCTGGCCAC‑GGCGTGGCCGGG‑GGT‑GCGCGGCCACCC‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTAACGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGa                       <  6:259407/149‑1 (MQ=255)
                                                                                                 cccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGA‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt                 >  8:101656/1‑148 (MQ=25)
                                                                                                  ccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt                 >  4:115949/1‑147 (MQ=37)
                                                                                                  ccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATAGCCATAAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCACGCTAACGAATCATGACTccca                 >  8:265790/1‑146 (MQ=25)
                                                                                                    gcgAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg              >  5:153282/1‑148 (MQ=37)
                                                                                                    gcgAAACAGGCGCCGCGGTGCATGACACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg              >  5:44983/1‑148 (MQ=37)
                                                                                                              cgccgcGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCaa   <  6:153282/149‑1 (MQ=37)
                                                                                                                 cgcgGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAg  >  1:367499/1‑147 (MQ=37)
                                                                                                                              ||                                                                                                                                         
CGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGT‑GTT‑TCG‑GG‑CA‑CG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAG  >  NC_002947_CJ‑RC/1499354‑1499611

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A