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 I1 R1 66 46.7 5280542 98.1% 5180211 47.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_017635 2,312,899 C→T G160G (GGG→GGA)  ECW_RS11560 ← phage tail sheath protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0176352,312,8990CT100.0% 14.9 / NA 5G160G (GGG→GGA) ECW_RS11560phage tail sheath protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (2/3);  total (2/3)

GCTTTCACCTCGGAAATGGTCTTACAGCCCCATGCGCTGATATACCCGAAAGCGCGCAGCTTCTGA  >  NC_017635/2312855‑2312920
                                            |                     
gCTTTCACCTCGGAAATGGTCTTACAGCCCCATGCGCTGATATAtcc                     >  2:1274367/1‑47 (MQ=255)
           ggAAATGGTCTTACAGCCCCATGCGCTGATATATCCGAAAGCGCGCAg         <  1:539541/48‑1 (MQ=255)
               aTGGTCTTACAGCCCCATGCGCTGATATATCCGAAAGCGCGCAGCTTc     >  1:1560841/1‑48 (MQ=255)
               aTGGTCTTACAGCCCCATGCGCTGATATATCCGAAAGCGCGCAGCTTc     <  2:1078573/48‑1 (MQ=255)
                  gTCTTACAGCCCCATGCGCTGATATATCCGAAAGCGCGCAGCTTCTg   <  2:2048599/47‑1 (MQ=255)
                    cTTACAGCCCCATGCGCTGATATATCCGAAAGCGCGCAGCTTCTGa  >  2:1808920/1‑46 (MQ=255)
                                            |                     
GCTTTCACCTCGGAAATGGTCTTACAGCCCCATGCGCTGATATACCCGAAAGCGCGCAGCTTCTGA  >  NC_017635/2312855‑2312920

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A