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 F1 I2 R1 884 257.2 12958910 96.9% 12557183 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,358,623 A→G intergenic (+372/‑188) gltD → / → gltF glutamate synthase small subunit/GltF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,358,6230AG100.0% 25.8 / NA 9intergenic (+372/‑188)gltD/gltFglutamate synthase small subunit/GltF
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (5/4);  total (5/4)

ATTATCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTATCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCAA  >  NC_000913/3358559‑3358704
                                                                |                                                                                 
attatCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCtt                                                       <  1:3078762/93‑1 (MQ=255)
  tatCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCttat                                                     >  2:1244732/1‑93 (MQ=255)
       ttAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTc                                                >  2:4399508/1‑93 (MQ=255)
               cTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATc                                        <  1:326481/93‑1 (MQ=255)
                       tttCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACtat                                <  1:6477199/93‑1 (MQ=255)
                              tttttCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTc                         >  2:5617677/1‑93 (MQ=255)
                                          aaCATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAaataaata             <  2:4907331/93‑1 (MQ=255)
                                              ttCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATc         >  2:2532054/1‑93 (MQ=255)
                                                     aaTGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCaa  >  1:4258366/1‑93 (MQ=255)
                                                                |                                                                                 
ATTATCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTATCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCAA  >  NC_000913/3358559‑3358704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
ATTATCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTATCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCAA  >  NC_000913/3358559‑3358704
                                                                |                                                                                 
ATTATCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTA                                                      <  SRR4302534.3159643/94‑1 (MQ=60)
               CTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCG                                       <  SRR4302534.334872/94‑1 (MQ=60)
                       TTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATA                               <  SRR4302534.6651730/94‑1 (MQ=60)
                                                    TAATGAATAATTGTCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCAA  >  SRR4302534.4373331/1‑94 (MQ=60)
                                                                |                                                                                 
ATTATCCTTAATTATCTATATATTTTCCTATTTTTCAGCGCAAACATTCATGTAATGAATAATTATCACCACAAACCACCTCACCAGCACCTTATTATTCACATGATCGTAACTATAAAATTCATTAAATAAATACATCCCAGCAA  >  NC_000913/3358559‑3358704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑