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 F3 I0 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,541,664 G→A 29.0% E129K (GAA→AAA)  crr → glucose‑specific enzyme IIA component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,541,6640GA29.0% 42.6 / 20.3 31E129K (GAA→AAA) crrglucose‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand):  ref base G (6/16);  new base A (6/3);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 5.62e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

TTGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAG  >  W3110S.gb/2541599‑2541724
                                                                 |                                                            
ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGaa                                                            >  1:2062806/1‑68 (MQ=255)
ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGaa                                                            >  1:2316257/1‑68 (MQ=255)
ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGaa                                                            >  1:2138364/1‑68 (MQ=255)
ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGaa                                                            >  1:2198069/1‑68 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:1357086/71‑1 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:1248756/71‑1 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:551414/71‑1 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:468746/71‑1 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:1972813/71‑1 (MQ=255)
             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:2003990/71‑1 (MQ=255)
              cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:2801621/70‑1 (MQ=255)
               aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTa                                            <  1:966960/69‑1 (MQ=255)
                 cgcgTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCt                                        <  1:1358250/71‑1 (MQ=255)
                 cgcgTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCt                                        <  1:793803/71‑1 (MQ=255)
                  gcgTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCt                                        <  1:2417455/70‑1 (MQ=255)
                       aaaGTTGGCGATGCTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACGCTGACTcc                                  >  1:545852/1‑71 (MQ=255)
                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                                  >  1:533953/1‑71 (MQ=255)
                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                                  >  1:96675/1‑71 (MQ=255)
                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                                  >  1:960714/1‑71 (MQ=255)
                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                                  >  1:2195393/1‑71 (MQ=255)
                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                                  >  1:3280089/1‑71 (MQ=255)
                                    cTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCt                                        <  1:510926/52‑1 (MQ=255)
                                    cTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCt                                        <  1:687643/52‑1 (MQ=255)
                                    cTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCt                                        <  1:1949253/52‑1 (MQ=255)
                                          ttGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa                   <  1:1481501/67‑1 (MQ=255)
                                          ttGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa                   <  1:602471/67‑1 (MQ=255)
                                          ttGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa                   <  1:660769/67‑1 (MQ=255)
                                          ttGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa                   <  1:2130016/67‑1 (MQ=255)
                                                        ccGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAg  >  1:360876/1‑70 (MQ=255)
                                                        ccGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAg  >  1:2677634/1‑70 (MQ=255)
                                                         cGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa                   <  1:1903651/52‑1 (MQ=255)
                                                                 |                                                            
TTGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAG  >  W3110S.gb/2541599‑2541724

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