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
A5 F28 I1 R1 826 0.0 88706 74.7% 66263 57.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,281,798 Δ1 bp intergenic (+318/‑33) agaA → / → agaS predicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,281,7960C.100.0% 304.0 / NA 79intergenic (+316/‑35)agaA/agaSpredicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (0/79);  total (0/79)

CACCAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGACAACGCCCGACGTCAAGTTCAT  >  W3110S.gb/3281754‑3281812
                                          |                
cACCAAGTGAGATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:8180/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68516/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:70212/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68453/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68095/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:65726/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:63308/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:62076/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:6142/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:59471/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:57621/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:50386/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:49918/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47858/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47594/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47542/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:11059/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47095/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:44002/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:81480/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:9247/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:87204/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:87084/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:85721/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:84907/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:84166/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:84065/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:83977/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47157/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:81197/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:78429/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:77631/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:75695/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:73382/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:72734/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:7079/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16575/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:23480/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:41493/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:20873/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:20536/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:1987/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:19856/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:17769/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:1704/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16688/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:20930/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16140/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:15630/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:13913/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:13797/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:13658/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:12679/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:12672/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:12497/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:33431/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:39757/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:38874/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:38773/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:37224/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:36576/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:35352/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:34537/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:23987/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:31821/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:29588/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:27310/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:25712/58‑1 (MQ=255)
cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:24793/58‑1 (MQ=255)
cACCAAGTGAAACGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:13420/58‑1 (MQ=255)
 aCCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:8681/57‑1 (MQ=255)
      gTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:57544/52‑1 (MQ=255)
        gaaatgaaaCGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:58505/50‑1 (MQ=255)
        gaaatgaaaCGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:21883/50‑1 (MQ=255)
         aaatgaaaCGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:53882/49‑1 (MQ=38)
          aatgaaaCGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:74395/48‑1 (MQ=38)
                  gAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:83526/40‑1 (MQ=37)
                   aaaGCCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47352/39‑1 (MQ=25)
                      ggCATGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16882/36‑1 (MQ=21)
                                          |                
CACCAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGACAACGCCCGACGTCAAGTTCAT  >  W3110S.gb/3281754‑3281812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A