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
A6 F28 I1 R1 191 83.5 2830284 99.3% 2810472 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,231,411 G→A intergenic (+172/‑254) ygjK → / → fadH glycoside hydrolase/2,4‑dienoyl‑CoA reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,231,4110GA100.0% 12.3 / NA 6intergenic (+172/‑254)ygjK/fadHglycoside hydrolase/2,4‑dienoyl‑CoA reductase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (4/2);  total (4/2)

GCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGG  >  NC_000913/3231379‑3231545
                                |                                                                                                                                      
gCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGAc                             <  1:420309/140‑1 (MQ=11)
                    ctggccGGATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCg                        <  1:172538/120‑1 (MQ=255)
                    ctggccGGATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCg                        >  2:172538/6‑125 (MQ=17)
                    ctggccGGATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTa         >  1:869998/6‑140 (MQ=255)
                           gATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCgg  >  1:1114231/1‑140 (MQ=255)
                           gATAAAACGCGGCAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCgg  >  1:850403/1‑140 (MQ=255)
                                |                                                                                                                                      
GCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGG  >  NC_000913/3231379‑3231545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A