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 F2 I211 R1 223 18.0 1007644 96.3% 970361 85.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,934,995 +C intergenic (‑308/‑173) yieP ← / → BW25113_RS19520 FadR/GntR family transcriptional regulator/16S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,934,9911.C87.5% 18.5 / ‑3.7 8intergenic (‑304/‑177)yieP/BW25113_RS19520FadR/GntR family transcriptional regulator/16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (5/2);  total (5/3)
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

ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT  >  NZ_CP009273/3934930‑3935075
                                                              |                                                                                    
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaagc                                                           <  2:274772/90‑1 (MQ=255)
 cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCg                                                          >  2:168395/1‑90 (MQ=255)
           gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc                                                                <  1:414186/74‑1 (MQ=255)
           gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc                                                                >  2:414186/1‑74 (MQ=255)
                                          gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa                 >  1:303455/1‑90 (MQ=255)
                                            gctggCGTATTATGCACA‑CCACGCGCCGCTGAGAAAAAGCAATGCGGCCCTGCTCTTTAACAATTTATCAAACAATCTGTGTCGGCtctc              <  1:297337/86‑1 (MQ=11)
                                                  gTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGa         >  1:29657/1‑90 (MQ=255)
                                                         gCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAt  >  1:361451/1‑90 (MQ=255)
                                                              |                                                                                    
ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT  >  NZ_CP009273/3934930‑3935075

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG  >  NZ_CP009273/3934925‑3935090
                                                                       |                                                                                               
agacagCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCAC                                                                     <  SRR3722094.421394/94‑1 (MQ=25)
                                     ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA                                >  SRR3722094.308155/1‑100 (MQ=24)
                                             GCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGA                        >  SRR3722094.30093/1‑100 (MQ=24)
                                                 gctgGCGTATTATGCACA‑CCACGCGCCGCTGAGAAAAAGCAATGCGGCCCTGCTCTTTAACAATTTATCAAACAATCTGTGTCGGCTCTCGAAGATccgc                   <  SRR3722094.301864/96‑5 (MQ=2)
                                                    AGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT                 >  SRR3722094.367507/1‑100 (MQ=8)
                                                            ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG         >  SRR3722094.458396/1‑100 (MQ=6)
                                                                  C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG  >  SRR3722094.177847/1‑100 (MQ=7)
                                                                       |                                                                                               
TGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG  >  NZ_CP009273/3934925‑3935090

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑