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 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,861,751 T→C 78.3% N423S (AAC→AGC)  lldP ← L‑lactate permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,861,7510TC78.3% 127.8 / 30.4 60N423S (AAC→AGC) lldPL‑lactate permease
Reads supporting (aligned to +/- strand):  ref base T (11/2);  new base C (27/20);  total (38/22)
Fisher's exact test for biased strand distribution p-value = 1.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGT  >  W3110S.gb/3861688‑3861818
                                                               |                                                                   
aagGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGaaa                                                               >  1:2502687/1‑70 (MQ=255)
aagGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGaaa                                                               >  1:1798500/1‑70 (MQ=255)
aagGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGaaa                                                               >  1:1584195/1‑70 (MQ=255)
aagGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGa                                                                 >  1:3530165/1‑68 (MQ=255)
 agGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATa                                                             <  1:110657/71‑1 (MQ=255)
 agGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATa                                                             <  1:1272824/71‑1 (MQ=255)
 agGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATa                                                             <  1:1531921/71‑1 (MQ=255)
    tGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAg                                                          >  1:985515/1‑71 (MQ=255)
       aTGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:2279702/71‑1 (MQ=255)
       aTGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:1342189/71‑1 (MQ=255)
       aTGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:1347132/71‑1 (MQ=255)
       aTGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:941128/71‑1 (MQ=255)
       aTGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:761124/71‑1 (MQ=255)
        tGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       >  1:1983623/1‑70 (MQ=255)
        tGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       >  1:3166534/1‑70 (MQ=255)
                   tgtgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:1731524/59‑1 (MQ=255)
                   tgtgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:683736/59‑1 (MQ=255)
                   tgtgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:761967/59‑1 (MQ=255)
                   tgtgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:109421/59‑1 (MQ=255)
                     tgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCAt                                         <  1:1003574/71‑1 (MQ=255)
                     tgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCAt                                         <  1:3564688/71‑1 (MQ=255)
                     tgCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCAt                                         <  1:397910/71‑1 (MQ=255)
                              gCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATg                                  >  1:2392554/1‑69 (MQ=255)
                               ccAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAg                                                          >  1:2254825/1‑44 (MQ=255)
                               ccAGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAg                                                          >  1:2479325/1‑44 (MQ=255)
                                 aGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                             <  1:355329/71‑1 (MQ=255)
                                 aGCGCCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTa                             <  1:3504683/71‑1 (MQ=255)
                                    gcCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGAt                          >  1:2137282/1‑71 (MQ=255)
                                    gcCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGAt                          >  1:1476785/1‑71 (MQ=255)
                                    gcCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGAt                          >  1:2973531/1‑71 (MQ=255)
                                    gcCAGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGAt                          >  1:3007462/1‑71 (MQ=255)
                                       aGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATggg                       <  1:1026872/71‑1 (MQ=255)
                                       aGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATggg                       >  1:1098373/1‑71 (MQ=255)
                                       aGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATggg                       >  1:146523/1‑71 (MQ=255)
                                       aGTGTTGATGACAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATg                         >  1:431146/1‑69 (MQ=255)
                                         tgtTGATGACAGTCCGGAATAGCTCGAAATAAAGGCg                                                       <  1:2554718/37‑1 (MQ=255)
                                             gatgaCAGTCCGGAATAGCTCGAAATAAAGTCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                 >  1:3339550/1‑71 (MQ=255)
                                              atgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                 <  1:1408526/70‑1 (MQ=255)
                                              atgaCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGc                 <  1:1897433/70‑1 (MQ=255)
                                               tgaCAGTCCGGAATAGCTCGAAATAACGGCGAATg                                                   >  1:3599598/1‑35 (MQ=38)
                                               tgaCAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                           >  1:485357/1‑59 (MQ=255)
                                               tgaCAGTCCGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGa                           >  1:489818/1‑59 (MQ=255)
                                                 aCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAg                               >  1:3503646/1‑53 (MQ=255)
                                                 aCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAg                               >  1:2867170/1‑53 (MQ=255)
                                                 aCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAg                               >  1:1774440/1‑53 (MQ=255)
                                                 aCAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAg                               >  1:649656/1‑53 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCa                                          >  1:417052/1‑36 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCa                                          >  1:3003072/1‑36 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCaga                   >  1:3163582/1‑59 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt        >  1:3071064/1‑70 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt        <  1:910736/70‑1 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt        >  1:1948568/1‑70 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCttt        >  1:2066545/1‑70 (MQ=255)
                                                       cGGAATAGCTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCtt         >  1:1573130/1‑69 (MQ=255)
                                                           aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGc    >  1:45445/1‑70 (MQ=255)
                                                           aTAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCg   >  1:3717260/1‑71 (MQ=255)
                                                            tAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCg   >  1:736868/1‑70 (MQ=255)
                                                            tAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGt  >  1:525851/1‑71 (MQ=255)
                                                            tAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGt  >  1:984031/1‑71 (MQ=255)
                                                            tAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGt  >  1:2995911/1‑71 (MQ=255)
                                                               |                                                                   
AAGGTGAATGCATGACCGGTGTGCGCCAGTGCCAGCGCCAGTGTTGATGACAGTCCGGAATAGTTCGAAATAAAGGCGAATGCCAGCACCATACCGATGGAGTAGATGGGCAGAGCCAGTTCTTTCAGCGT  >  W3110S.gb/3861688‑3861818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A