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 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,068,392 T→C 33.3% 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.gb4,068,3920TC33.3% 110.0 / 92.5 96M493T (ATG→ACG) glgB1,4‑alpha‑glucan branching enzyme
Reads supporting (aligned to +/- strand):  ref base T (24/40);  new base C (17/15);  total (41/55)
Fisher's exact test for biased strand distribution p-value = 1.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

GGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTACA  >  W3110S.gb/4068331‑4068460
                                                             |                                                                    
ggCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGa                                                             >  1:2949904/1‑71 (MQ=255)
ggCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGa                                                             >  1:76208/1‑71 (MQ=255)
       ttggCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGtt                                                      >  1:2446861/3‑71 (MQ=255)
         ggCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGttt                                                     <  1:3338305/70‑1 (MQ=255)
           cTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATc                                                  <  1:2218585/71‑1 (MQ=255)
           cTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCGCGACCCGGTTTATc                                                  <  1:3009424/71‑1 (MQ=255)
              cTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTTGACTACATGAAGCTCGACCCGGTTTATCg                                                 <  1:1070809/69‑1 (MQ=255)
              cTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACAt                                                                      >  1:378959/1‑48 (MQ=255)
              cTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCg                                                 <  1:1154194/69‑1 (MQ=255)
              cTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGt                                                >  1:2530919/1‑70 (MQ=255)
              cTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGt                                                >  1:640164/1‑70 (MQ=255)
                    cAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:738328/1‑70 (MQ=255)
                    cAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:1406156/1‑70 (MQ=255)
                    cAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:266597/1‑70 (MQ=255)
                     aaGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTatca                                        >  1:127406/1‑71 (MQ=255)
                      aGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTatcat                                       <  1:317250/71‑1 (MQ=255)
                        tGGAACCTCGGCTGTATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:599608/55‑1 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTa                                           <  1:173750/65‑1 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTAtcatca                                     >  1:920619/1‑71 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTAtcatca                                     >  1:2705682/1‑71 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTAtcatca                                     >  1:1698153/1‑71 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTAtaatca                                     >  1:842509/1‑71 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGCCCCGGTTTATCGTCAGTAtcatca                                     >  1:494947/1‑71 (MQ=255)
                        tGGAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTAtcatca                                     >  1:1984786/1‑71 (MQ=255)
                          gAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    >  1:3515403/1‑70 (MQ=255)
                          gAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:1455600/70‑1 (MQ=255)
                          gAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:3513982/70‑1 (MQ=255)
                          gAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCg                                                         >  1:1456295/1‑49 (MQ=255)
                          gAACCTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    >  1:3251664/1‑70 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:1389397/50‑1 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:4039957/50‑1 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:341305/50‑1 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:2173164/50‑1 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:2362457/71‑1 (MQ=255)
                             ccTCGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATAATCACGAt                                 >  1:3848345/1‑70 (MQ=255)
                              cTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGttt                                                     <  1:989724/49‑1 (MQ=255)
                              cTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaa                               <  1:3879266/71‑1 (MQ=255)
                               tCGGCTGGATGCATGACACACTGGAGTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaa                               >  1:1327243/1‑70 (MQ=255)
                                cGGCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaa                               <  1:3333747/69‑1 (MQ=255)
                                  gCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                           <  1:1015200/71‑1 (MQ=255)
                                  gCTGGATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                           <  1:3989066/71‑1 (MQ=255)
                                    tGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTAt                                                   <  1:16565/45‑1 (MQ=255)
                                      gATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTatcat                                       <  1:2981326/55‑1 (MQ=255)
                                      gATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGAt                                 <  1:3574135/61‑1 (MQ=255)
                                      gATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGAt                                 <  1:719921/61‑1 (MQ=255)
                                      gATGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGAt                                 <  1:4010185/61‑1 (MQ=255)
                                       aTGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:1620101/1‑51 (MQ=255)
                                       aTGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:4053771/1‑51 (MQ=255)
                                       aTGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTat                                          >  1:3582546/1‑51 (MQ=255)
                                       aTGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                           >  1:3669271/1‑50 (MQ=255)
                                       aTGCATGACACCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTa                                           >  1:4058205/1‑50 (MQ=255)
                                        tGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTat                                          <  1:3753611/50‑1 (MQ=255)
                                        tGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTat                                          <  1:2722934/50‑1 (MQ=255)
                                        tGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTat                                          <  1:447642/50‑1 (MQ=255)
                                          cATGACACCCTGGTCTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCgg                   <  1:1658739/71‑1 (MQ=255)
                                          cATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                              >  1:3341851/1‑60 (MQ=255)
                                          cATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                              >  1:1903387/1‑60 (MQ=255)
                                           aTGACACCCTGGTCTACACGAAGCTCGACCCGGTTTCTCGGCAGTATCATCACGATAAACTGACCTTCgg                   <  1:3570732/70‑1 (MQ=255)
                                           aTGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCggg                  <  1:4063086/71‑1 (MQ=255)
                                            tGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:2801425/56‑1 (MQ=255)
                                              acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGaa                >  1:1775171/1‑69 (MQ=255)
                                              acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAtt               >  1:2025034/1‑71 (MQ=255)
                                              acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAtt               >  1:2908674/1‑71 (MQ=255)
                                              acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAt                <  1:1165774/70‑1 (MQ=255)
                                              acacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGAt                >  1:2894999/1‑70 (MQ=255)
                                               cacCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtc              <  1:3089105/71‑1 (MQ=255)
                                               cacCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtc              <  1:1528329/71‑1 (MQ=255)
                                                acCCTGGACTACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtc              <  1:2438763/70‑1 (MQ=255)
                                                 cccTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtctc            >  1:639940/1‑71 (MQ=255)
                                                   cTGGACTACATGAAGCTCGACCCGGTTTATCGTCAg                                             <  1:898439/36‑1 (MQ=255)
                                                   cTGGACTACATGAAGCTCGACCCGGTTTATCGTCAg                                             <  1:2922452/36‑1 (MQ=255)
                                                   cTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:994416/45‑1 (MQ=255)
                                                   cTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:3815882/49‑1 (MQ=255)
                                                    tGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtctc            <  1:3410114/68‑1 (MQ=255)
                                                    tGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtctc            <  1:2501108/68‑1 (MQ=255)
                                                     ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                              >  1:3854427/1‑49 (MQ=255)
                                                     ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                              >  1:2514230/1‑49 (MQ=255)
                                                     ggACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATaaa                              >  1:337243/1‑49 (MQ=255)
                                                      gACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTa          >  1:1792623/1‑68 (MQ=255)
                                                      gACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTAc         <  1:1251049/69‑1 (MQ=255)
                                                      gACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACaa       >  1:466480/1‑71 (MQ=255)
                                                       aCTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATtc              <  1:293765/63‑1 (MQ=255)
                                                         tACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:3584893/43‑1 (MQ=255)
                                                         tACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:2429276/43‑1 (MQ=255)
                                                         tACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATa                                <  1:3659517/43‑1 (MQ=255)
                                                         tACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTAc         <  1:324244/66‑1 (MQ=255)
                                                         tACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:439077/39‑1 (MQ=255)
                                                         tACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:2861769/39‑1 (MQ=255)
                                                         tACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:2857070/39‑1 (MQ=255)
                                                         tACACGAAGCTCGACCCGGTTTATCGTCAGTATCATCAc                                    <  1:1041887/39‑1 (MQ=255)
                                                           cATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTaca  >  1:3829723/1‑71 (MQ=255)
                                                           cATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTaca  >  1:844382/1‑71 (MQ=255)
                                                           cATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTaca  >  1:227881/1‑71 (MQ=255)
                                                           cATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTac   >  1:4024887/1‑70 (MQ=255)
                                                            aTGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                           <  1:564057/45‑1 (MQ=255)
                                                            aTGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                           <  1:3788957/45‑1 (MQ=255)
                                                            aTGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTg                           <  1:3538349/45‑1 (MQ=255)
                                                             |                                                                    
GGCGGTCTGGGCTTCTGGTACAAGTGGAACCTCGGCTGGATGCATGACACCCTGGACTACATGAAGCTCGACCCGGTTTATCGTCAGTATCATCACGATAAACTGACCTTCGGGATTCTCTACAACTACA  >  W3110S.gb/4068331‑4068460

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