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 3,281,782 T→C intergenic (+302/‑49) 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.gb3,281,7820TC85.0% 122.4 / 3.5 93intergenic (+302/‑49)agaA/agaSpredicted truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
Reads supporting (aligned to +/- strand):  ref base T (0/14);  new base C (0/79);  total (0/93)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTCTATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGACAACGCCCGACGTCAAGTTCAT  >  W3110S.gb/3281724‑3281812
                                                          |                              
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:26638/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:65762/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:29739/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:32839/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:58835/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:40570/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:81211/61‑1 (MQ=255)
tttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:4823/61‑1 (MQ=255)
 ttctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:78463/60‑1 (MQ=255)
  tctATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:41012/59‑1 (MQ=255)
     ataGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:37112/56‑1 (MQ=255)
     ataGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:36520/56‑1 (MQ=255)
        gATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:23013/53‑1 (MQ=255)
        gATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGa                              <  1:41124/53‑1 (MQ=255)
                              cACCAAGTGAGATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:8180/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:59471/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47157/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47542/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:63308/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47594/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:62076/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:6142/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:57621/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68095/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:50386/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47858/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:49918/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:78429/58‑1 (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  <  1:81480/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:81197/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:65726/58‑1 (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  <  1:70212/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68516/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:68453/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:44002/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:17769/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:23987/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:23480/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:47095/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:20930/58‑1 (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  <  1:24793/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:1704/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16688/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16575/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:16140/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:13658/58‑1 (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  <  1:36576/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:12497/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:11059/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:41493/58‑1 (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  <  1:12672/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:25712/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:12679/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:35352/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:34537/58‑1 (MQ=255)
                              cACCAAGTGAAATGAAACGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:33431/58‑1 (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)
                              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  <  1:21883/50‑1 (MQ=255)
                                      gaaatgaaaCGAAAGGCAAGCGAAAGCGACAACG‑CCGACGTCAAGTtcat  <  1:58505/50‑1 (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)
                                                          |                              
TTTCTATAGATTTTAATCAACGAAAGACATCACCAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGACAACGCCCGACGTCAAGTTCAT  >  W3110S.gb/3281724‑3281812

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