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 I197 R1 189 12.7 697584 97.1% 677354 86.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,505,777 T→C I137V (ATC→GTC)  mntH ← Nramp family divalent metal transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,505,7770TC88.9% 17.4 / ‑3.5 9I137V (ATC→GTC) mntHNramp family divalent metal transporter
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (3/5);  total (4/5)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01

CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATA  >  NZ_CP009273/2505690‑2505847
                                                                                       |                                                                      
cgGCAACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGAccc                                                                      <  1:133614/90‑1 (MQ=255)
     acaaacaaCAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTc                                                                 <  1:134767/90‑1 (MQ=255)
                     cGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGca                                                 <  2:182324/90‑1 (MQ=255)
                      gCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGcaa                                                >  1:338492/1‑90 (MQ=255)
                                         ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg                             <  1:247819/90‑1 (MQ=255)
                                         ggTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATg                             <  2:267864/90‑1 (MQ=255)
                                            ttttGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGt                          >  1:204820/1‑90 (MQ=255)
                                                             cagcaTTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccgc         <  2:169636/90‑1 (MQ=255)
                                                                 aTTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCa     >  2:331853/1‑90 (MQ=255)
                                                                    aaaaTCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATa  >  1:156744/1‑90 (MQ=255)
                                                                                       |                                                                      
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATA  >  NZ_CP009273/2505690‑2505847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATA  >  NZ_CP009273/2505690‑2505847
                                                                                       |                                                                      
CGGCAACAAACAACAGTACCCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCAC                                                            <  SRR3722076.135173/100‑1 (MQ=60)
     ACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGC                                                       <  SRR3722076.136342/100‑1 (MQ=60)
            ACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAA                                                >  SRR3722076.343638/1‑100 (MQ=60)
                                  CTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGT                          >  SRR3722076.207454/1‑100 (MQ=60)
                                         GGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAAC                   <  SRR3722076.251363/100‑1 (MQ=60)
                                                          TTGCAGCATTAAAATCAGGAAAGTCGCGACCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATA  >  SRR3722076.158604/1‑100 (MQ=60)
                                                                                       |                                                                      
CGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATA  >  NZ_CP009273/2505690‑2505847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑