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 F3 I95 R1 196 14.2 808436 96.0% 776098 85.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,632,437 (T)7→6 intergenic (‑71/+8) BW25113_RS08135 ← / ← BW25113_RS25620 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,632,4310T.100.0% 59.0 / NA 15intergenic (‑65/+14)BW25113_RS08135/BW25113_RS25620hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (7/8);  total (7/8)

GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGA  >  NZ_CP009273/1632353‑1632502
                                                                              |                                                                       
ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat                                                             <  1:343060/90‑1 (MQ=255)
ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat                                                             <  2:402953/90‑1 (MQ=255)
        aCGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt                                                     <  1:65412/90‑1 (MQ=255)
                            cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGa                                 >  1:160007/1‑90 (MQ=255)
                             aGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt                                                     <  1:271493/69‑1 (MQ=255)
                             aGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt                                                     >  2:271493/1‑69 (MQ=255)
                              gTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAAt                               >  1:115602/1‑90 (MQ=255)
                                cATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAg                             >  2:295424/1‑90 (MQ=255)
                                       ggCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCaa                      <  2:114788/90‑1 (MQ=255)
                                                   gctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGt                                                           <  1:34613/41‑1 (MQ=39)
                                                   gctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGt                                                           >  2:34613/1‑41 (MQ=39)
                                                   gctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtag                                                   >  1:258694/1‑49 (MQ=39)
                                                   gctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtag                                                   <  2:258694/49‑1 (MQ=39)
                                                     tgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTccc        >  2:66235/1‑90 (MQ=255)
                                                           agagTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGa  <  1:244637/90‑1 (MQ=255)
                                                                              |                                                                       
GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGA  >  NZ_CP009273/1632353‑1632502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTT  >  NZ_CP009273/1632353‑1632512
                                                                                    |                                                                           
GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAG                                                             <  SRR3722235.347992/100‑1 (MQ=60)
  ctcttgtctcgtgggctcggagatgtgtataagagacaGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTA                                                           <  SRR3722235.34995/62‑1 (MQ=60)
        ataagagacaGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG                                                     <  SRR3722235.275169/90‑1 (MQ=60)
        ACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG                                                     <  SRR3722235.66156/100‑1 (MQ=60)
                  GTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGA                                           >  SRR3722235.161847/1‑100 (MQ=60)
                    GTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAAT                                         >  SRR3722235.116941/1‑100 (MQ=60)
                                         CACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTActgtctcttatacacatctccgagcccacga                    >  SRR3722235.262100/1‑69 (MQ=60)
                                                           AGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTT  <  SRR3722235.247762/100‑1 (MQ=60)
                                                                                    |                                                                           
GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTT  >  NZ_CP009273/1632353‑1632512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑