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 3,861,751 T→C 9.0% N423S (AAC→AGC)  lldP ← L‑lactate permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,861,7510TC 9.0% 233.7 / 10.8 78N423S (AAC→AGC) lldPL‑lactate permease
Reads supporting (aligned to +/- strand):  ref base T (56/15);  new base C (2/5);  total (58/20)
Fisher's exact test for biased strand distribution p-value = 1.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.03e-01

TGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGTGC  >  W3110S.gb/3861696‑3861820
                                                       |                                                                     
tGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGc                                                          >  1:639512/1‑69 (MQ=255)
tGCATGACCGGTGTGCGCCAGTGACAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCg                                                         >  1:2658054/1‑70 (MQ=255)
                gcCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATAcc                                        <  1:2702941/71‑1 (MQ=255)
                gcCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATAcc                                        <  1:3103925/71‑1 (MQ=255)
                gcCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATAcc                                        <  1:409612/71‑1 (MQ=255)
                gcCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATAcc                                        <  1:342734/71‑1 (MQ=255)
                gcCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATAcc                                        <  1:3248261/71‑1 (MQ=255)
                                gtgtTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATggg                         >  1:2820732/1‑70 (MQ=255)
                                gtgtTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATggg                         >  1:388894/1‑70 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCATCACCATACCGATGGAGTa                               <  1:3083826/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:2407425/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:2297103/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:3053954/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:1615670/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:1568324/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:3141305/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:451247/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:1208742/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:1090874/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:977472/61‑1 (MQ=255)
                                   ttGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCACCACCATACCGATGGAGTa                               <  1:389169/61‑1 (MQ=255)
                                   ttGATGACAGGCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:2610382/61‑1 (MQ=255)
                                    tgatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               <  1:2778568/60‑1 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                               >  1:3353378/1‑59 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:620752/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:294561/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:74615/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:817655/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:101449/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:1670725/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:1243732/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:153646/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:2028364/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:1133628/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:1349928/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                             >  1:1822187/1‑61 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:1727861/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:2406365/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:917668/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:950934/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:2806364/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:2759302/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:2053047/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:1321206/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:1302188/1‑71 (MQ=255)
                                     gatgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:605320/1‑71 (MQ=255)
                                            gTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCt            <  1:2725285/71‑1 (MQ=255)
                                               cGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt          >  1:853781/1‑70 (MQ=255)
                                               cGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt          >  1:1006727/1‑70 (MQ=255)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATAGCGATGGAGTAGATGGGCAGAGc                   >  1:898079/1‑57 (MQ=255)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTATATGGGCACAGc                   >  1:1210898/1‑57 (MQ=39)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:3173206/1‑57 (MQ=255)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:541717/1‑57 (MQ=255)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:2814935/1‑57 (MQ=255)
                                                   aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                   >  1:1337959/1‑57 (MQ=255)
                                                      gTTCGAGATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:715/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGGACCATACCGATGGAGTAg                              >  1:1157048/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCCCCATACCGATGGAGTAGTTGGGCAGAGCCAGTTCTTTCAGCGt    >  1:906906/1‑69 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:3015460/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2447572/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2462445/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2545950/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2317085/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2773322/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2809527/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:2844047/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:1768493/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAg                              >  1:3022319/1‑43 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:1626821/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:522844/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:1304339/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:1455427/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:1484369/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:3183334/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:2938453/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:2918536/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:1785531/1‑71 (MQ=255)
                                                      gTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGtgc  >  1:2382741/1‑71 (MQ=255)
                                                       |                                                                     
TGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGTGC  >  W3110S.gb/3861696‑3861820

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