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 I230 R1 226 18.8 1048726 96.7% 1014118 86.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,230,259 C→T intergenic (‑86/‑135) nhaB ← / → fadR Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,230,2590CT87.5% 18.2 / ‑3.6 8intergenic (‑86/‑135)nhaB/fadRNa(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (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 = 1.74e-01

TGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCT  >  NZ_CP009273/1230176‑1230344
                                                                                   |                                                                                     
tgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATa                                                                                 >  1:451878/1‑90 (MQ=255)
    ttCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCa                                                                             >  1:382366/1‑90 (MQ=255)
     tCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCaa                                                                            <  1:510819/90‑1 (MQ=255)
          taccttacAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGa                                                                       >  1:47872/1‑90 (MQ=255)
                 cAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGAt                                                                <  2:439981/90‑1 (MQ=255)
                           atgatgTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATg                                                      >  2:255565/1‑90 (MQ=255)
                                                                         tGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGtt        <  2:34757/90‑1 (MQ=255)
                                                                               aaGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCct  >  1:439105/1‑90 (MQ=255)
                                                                                   |                                                                                     
TGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCT  >  NZ_CP009273/1230176‑1230344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA  >  NZ_CP009273/1230166‑1230356
                                                                                             |                                                                                                 
ATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATA                                                                                             >  SRR3722114.457513/1‑100 (MQ=60)
    CCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCA                                                                                         >  SRR3722114.386981/1‑100 (MQ=60)
          TGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGA                                                                                   >  SRR3722114.48343/1‑100 (MQ=60)
               TCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAG                                                                              <  SRR3722114.517221/100‑1 (MQ=60)
                                                                     CGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgcc                        >  SRR3722114.44118/1‑46 (MQ=60)
                                                                               GGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCT              >  SRR3722114.444518/1‑100 (MQ=60)
                                                                                           GTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA  >  SRR3722114.174546/1‑100 (MQ=60)
                                                                                             |                                                                                                 
ATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA  >  NZ_CP009273/1230166‑1230356

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑