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
A2 F1 I1 R1 182 31.9 1789978 98.5% 1763128 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,995,368 T→G pseudogene (653/707 nt) ygeN ← putative type III secretion system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,995,3680TG100.0% 20.8 / NA 7pseudogene (653/707 nt)ygeNputative type III secretion system protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (5/2);  total (5/2)

ATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAA  >  NC_000913/2995291‑2995437
                                                                             |                                                                     
aTCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTGTc                                                                     >  1:505602/1‑80 (MQ=255)
   aTTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAGGAATGTGTGTCaaa                                                                  <  1:505590/80‑1 (MQ=255)
        aCTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTGTCAAACAtttt                                                            >  1:505601/1‑81 (MQ=255)
             aGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTGTCAAACATTTTTTCaa                                                       >  2:505603/1‑81 (MQ=255)
                                cTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTGTCAAACATTTTTTCAACTAAATAATGTCTGGCtt                                     <  1:505591/80‑1 (MQ=255)
                                             aaaaCAGAATTATTCATATCCAAAGAATGTGTGTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg                       >  2:505607/1‑81 (MQ=255)
                                                                  aaaGAATGTGTGTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGaaa  >  1:505611/1‑81 (MQ=255)
                                                                             |                                                                     
ATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAA  >  NC_000913/2995291‑2995437

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A