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 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,068,392 T→C 29.5% M493T (ATG→ACG)  glgB → 1,4‑alpha‑glucan branching enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,068,3920TC29.5% 83.3 / 48.9 61M493T (ATG→ACG) glgB1,4‑alpha‑glucan branching enzyme
Reads supporting (aligned to +/- strand):  ref base T (20/23);  new base C (14/4);  total (34/27)
Fisher's exact test for biased strand distribution p-value = 4.63e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

ATATGGGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTACACT  >  W3110S.gb/4068326‑4068462
                                                                  |                                                                      
atatGGGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAg                                                                    >  1:3817594/1‑71 (MQ=255)
 tatGGGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGc                                                                   >  1:4551253/1‑71 (MQ=255)
   tGGGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTc                                                                 >  1:2386830/1‑71 (MQ=255)
     ggCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCg                                                                <  1:2061853/70‑1 (MQ=255)
     ggCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGa                                                               <  1:1497472/71‑1 (MQ=255)
     ggCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGa                                                               >  1:4306869/1‑71 (MQ=255)
            tGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGtt                                                        >  1:4037359/1‑71 (MQ=255)
            tGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGtt                                                        >  1:3105439/1‑71 (MQ=255)
              ggCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGtt                                                        <  1:3410588/69‑1 (MQ=255)
                      gTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACAt                                                                        <  1:4437700/45‑1 (MQ=255)
                      gTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTc                                                 <  1:1747625/68‑1 (MQ=255)
                       tACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                             <  1:4039927/71‑1 (MQ=255)
                        aCAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTat                                            >  1:53535/1‑71 (MQ=255)
                         cAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTc                                                                 >  1:3480512/1‑49 (MQ=255)
                         cAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTat                                            <  1:3551329/70‑1 (MQ=255)
                          aaGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTatca                                          <  1:2622649/71‑1 (MQ=255)
                             tGGAACCTCGGCTCGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTatcat                                         <  1:3847596/69‑1 (MQ=255)
                                 aCCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAg                                               >  1:2807679/1‑59 (MQ=255)
                                  ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCgg                                                          <  1:1227199/47‑1 (MQ=255)
                                  ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                  <  1:113702/71‑1 (MQ=255)
                                   cTCGGCTGGATGCATGACCCCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaa                                 <  1:966385/71‑1 (MQ=255)
                                   cTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTAtcatca                                       >  1:3639782/1‑65 (MQ=255)
                                   cTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                  <  1:2183576/70‑1 (MQ=255)
                                   cTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAg                                               >  1:2040620/1‑57 (MQ=255)
                                    tCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGa                                                               >  1:1909167/1‑40 (MQ=255)
                                     cGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                                >  1:4574149/1‑70 (MQ=255)
                                     cGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAg                                               >  1:1514770/1‑55 (MQ=255)
                                      ggCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                  <  1:498406/67‑1 (MQ=255)
                                      ggCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACt                              <  1:273629/71‑1 (MQ=255)
                                      ggCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACt                              <  1:1745633/71‑1 (MQ=255)
                                       gCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                                <  1:3973299/68‑1 (MQ=255)
                                       gCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                             <  1:4191868/71‑1 (MQ=255)
                                          ggATGCATGACACCCTGGACTACACGAAGCTCGACCCGGtt                                                        >  1:3440413/1‑41 (MQ=255)
                                           gATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTc                                                 <  1:2052514/47‑1 (MQ=255)
                                             tGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTAt                                                     >  1:657947/1‑41 (MQ=255)
                                               cATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                            >  1:2429992/1‑48 (MQ=255)
                                               cATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                            >  1:1415617/1‑48 (MQ=255)
                                               cATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                            >  1:1519456/1‑48 (MQ=255)
                                                aTGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCgg                     <  1:2705180/70‑1 (MQ=255)
                                                 tGACTCCCTGGACTACATGAAGCTCGACCCTGTTTATCGTCAGTatc                                           <  1:1147207/47‑1 (MQ=39)
                                                 tGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTc                                                 <  1:3304213/41‑1 (MQ=255)
                                                 tGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGa                                    <  1:1371841/54‑1 (MQ=255)
                                                 tGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGa                                    <  1:2869008/54‑1 (MQ=255)
                                                   acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCgg                     >  1:2315396/1‑67 (MQ=255)
                                                   acacCCTGGACTACATGAAGCTAGACCCGGTTTATCGTCAg                                               >  1:1794392/1‑41 (MQ=255)
                                                   acacCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                             >  1:3079013/1‑43 (MQ=255)
                                                   acacCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                             >  1:530513/1‑43 (MQ=255)
                                                   acacCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                                >  1:2084887/1‑56 (MQ=255)
                                                    cacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGAc                           >  1:3061619/1‑60 (MQ=255)
                                                         tGGACTACATGAAGCTCGACCCGGGTTATCGTCAGTatca                                          >  1:2169104/1‑40 (MQ=255)
                                                          ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAt                  <  1:958433/63‑1 (MQ=255)
                                                          ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTAc           >  1:702432/1‑70 (MQ=255)
                                                          ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGAACTTCGGGa                   >  1:46425/1‑62 (MQ=255)
                                                          ggACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                             >  1:1410595/1‑36 (MQ=255)
                                                          ggACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTa            >  1:3636316/1‑69 (MQ=255)
                                                           gACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTAc           <  1:4492034/69‑1 (MQ=255)
                                                           gACTACATGAAGCTCGACCAGGTTTATCGTCAGTATCATCACGATaaa                                >  1:3001212/1‑48 (MQ=255)
                                                           gACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAATCTCTACaa         >  1:3820898/1‑71 (MQ=255)
                                                              tACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                      <  1:4266853/39‑1 (MQ=255)
                                                                cATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTaca    <  1:2715395/71‑1 (MQ=255)
                                                                 aTGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTa            >  1:1446140/1‑62 (MQ=255)
                                                                 aTGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTacac   >  1:1896501/1‑71 (MQ=255)
                                                                  tGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTACACt  >  1:1793205/1‑71 (MQ=255)
                                                                  |                                                                      
ATATGGGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTACACT  >  W3110S.gb/4068326‑4068462

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