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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,826,300 G→A 16.5% D8D (GAC→GAT)  hydN ← formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,826,3000GA16.5% 215.5 / 31.3 91D8D (GAC→GAT) hydNformate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
Reads supporting (aligned to +/- strand):  ref base G (40/36);  new base A (10/5);  total (50/41)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

TCCTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTCACA  >  minE/1826232‑1826366
                                                                    |                                                                  
tCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTc                                                                  <  1:2760197/71‑1 (MQ=255)
   tGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATccg                                                                >  1:3303453/1‑68 (MQ=255)
     aTTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCaa                                                             >  1:2801771/1‑71 (MQ=255)
     aTTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCaa                                                             >  1:1252820/1‑71 (MQ=255)
     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATccg                                                                >  1:2860902/1‑66 (MQ=255)
     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGc                                                               <  1:1301137/69‑1 (MQ=255)
     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaa                                                             >  1:2380664/1‑71 (MQ=255)
     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaa                                                             >  1:2167744/1‑71 (MQ=255)
     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaa                                                             >  1:2018472/1‑71 (MQ=255)
      ttttCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAat                                                            <  1:1880420/71‑1 (MQ=255)
       tttCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTc                                                                  <  1:1525199/64‑1 (MQ=255)
           cTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGc                                                               <  1:184737/63‑1 (MQ=255)
           cTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAAtgatga                                                       <  1:585801/71‑1 (MQ=255)
            tgatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaa                                                      >  1:3912037/1‑71 (MQ=255)
             gatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaac                                                     >  1:829433/1‑70 (MQ=255)
              atgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaac                                                     <  1:3390769/70‑2 (MQ=255)
               tgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACg                                                   >  1:3370607/1‑71 (MQ=255)
                gagaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCaa                                                             >  1:1160774/1‑60 (MQ=255)
                 agaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                                 >  1:1502972/1‑71 (MQ=255)
                 agaAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                                 <  1:3194102/71‑1 (MQ=255)
                  gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:3120871/1‑62 (MQ=255)
                  gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:529211/1‑62 (MQ=255)
                  gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:2146661/1‑62 (MQ=255)
                  gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                                 >  1:2359820/1‑70 (MQ=255)
                   aaaCCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGtt                                                >  1:2441630/1‑70 (MQ=255)
                    aaCCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAAtgatga                                                       <  1:3015079/62‑1 (MQ=255)
                     actgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcat                                             <  1:1392119/68‑1 (MQ=255)
                      ccGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcat                                             >  1:221195/1‑70 (MQ=255)
                       tgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCa                                                              >  1:3328465/2‑52 (MQ=255)
                       tgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCa                                                              >  1:729198/2‑52 (MQ=255)
                       tgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatga                                           >  1:3730334/2‑69 (MQ=255)
                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcat                                             >  1:135977/1‑67 (MQ=255)
                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCaaa                                         <  1:201223/71‑1 (MQ=255)
                          gcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAt                                        >  1:2888500/1‑71 (MQ=255)
                          gcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAt                                        <  1:384788/71‑1 (MQ=255)
                           cACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       <  1:2533518/71‑1 (MQ=255)
                            aCGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcat                                             >  1:850961/1‑64 (MQ=255)
                            aCGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtc                                      >  1:3439196/1‑71 (MQ=255)
                            aCGCTACTTCACAAGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtc                                      <  1:768890/71‑1 (MQ=255)
                               cTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                                     >  1:509398/1‑53 (MQ=255)
                                tACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                                  <  1:731494/55‑1 (MQ=255)
                                  cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtctc                                    >  1:623207/1‑67 (MQ=255)
                                  cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAg                                 >  1:1524017/1‑70 (MQ=255)
                                   ttCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatg                                            <  1:3913877/58‑2 (MQ=255)
                                   ttCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCaa                                          <  1:520772/60‑1 (MQ=255)
                                   ttCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAt                                        <  1:1090971/62‑1 (MQ=255)
                                    tCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtc                                      >  1:3817360/1‑63 (MQ=255)
                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                             >  1:846647/1‑71 (MQ=255)
                                      acaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAACCGTTtcatca                                           <  1:2554902/56‑1 (MQ=39)
                                      acaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                             <  1:150715/70‑1 (MQ=255)
                                       caGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCgg                                                  <  1:303072/48‑1 (MQ=255)
                                       caGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCTAATTCTCCAGCAAt                             <  1:1971432/69‑1 (MQ=255)
                                       caGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGa                           <  1:1440278/71‑1 (MQ=255)
                                         ggTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAg                                 <  1:502951/63‑1 (MQ=255)
                                         ggTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGa                           >  1:3907000/1‑69 (MQ=255)
                                         gctACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         <  1:1055475/69‑1 (MQ=255)
                                          gTACGGCAACCAATACATTTACTCGCGTCAGCAatg                                                           <  1:1999394/36‑1 (MQ=255)
                                          gTACGGCAACCAATACATTTACTCGCGTCAGCAatg                                                           <  1:2897238/36‑1 (MQ=255)
                                          gTACGGCAACCAATACATTTACTCGCGTCAGCAatg                                                           <  1:2496556/36‑1 (MQ=255)
                                          gTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         >  1:648548/1‑70 (MQ=255)
                                            aCGGCAGCCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         >  1:1444928/1‑68 (MQ=255)
                                            aCGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       >  1:711479/1‑70 (MQ=255)
                                            aCGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       >  1:3329676/1‑70 (MQ=255)
                                            aCGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       >  1:3359709/1‑70 (MQ=255)
                                             cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt                      >  1:3017681/1‑70 (MQ=255)
                                             cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       <  1:2447215/69‑1 (MQ=255)
                                             cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTa                     <  1:1711542/71‑1 (MQ=255)
                                             cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTa                     <  1:2747809/71‑1 (MQ=255)
                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtctc                                    >  1:2940169/1‑55 (MQ=255)
                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAg                                 >  1:3127079/1‑58 (MQ=255)
                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt                      <  1:3891812/69‑1 (MQ=255)
                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    >  1:3091133/1‑71 (MQ=255)
                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    >  1:1368568/1‑71 (MQ=255)
                                                cAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATg                  >  1:2650426/1‑71 (MQ=255)
                                                 aaCCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt                      <  1:3336418/66‑1 (MQ=255)
                                                  aCCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATgcg                >  1:2225650/1‑71 (MQ=255)
                                                    cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATgcgc               >  1:1958373/1‑70 (MQ=255)
                                                    cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGcc              >  1:3370349/1‑71 (MQ=255)
                                                    cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTAAAGCAATGACAGTTAATgcgc               >  1:749488/1‑70 (MQ=255)
                                                      aTACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGa            >  1:2081039/1‑71 (MQ=255)
                                                       tACATTTACTCGCGTCAGCAATGATGAAACGGTtc                                               <  1:731826/35‑1 (MQ=255)
                                                       tACATTTACTCGCGTCAGCAATGATGAAACGGTtc                                               <  1:774138/35‑1 (MQ=255)
                                                       tACATTTACTCGCGTCAGCAATGATGAAACGGTtc                                               <  1:2571838/35‑1 (MQ=255)
                                                        aCATTTTCTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       >  1:509871/1‑42 (MQ=255)
                                                         cATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATa          >  1:3776683/1‑70 (MQ=255)
                                                          aTTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         <  1:2793440/54‑1 (MQ=255)
                                                          aTTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         <  1:1366945/54‑1 (MQ=255)
                                                          aTTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACa                         <  1:2078854/54‑1 (MQ=255)
                                                          aTTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACa        <  1:1513062/71‑1 (MQ=255)
                                                            ttACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGa                           >  1:2258391/1‑50 (MQ=255)
                                                              aCTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTcc                                   <  1:31010/40‑1 (MQ=255)
                                                                  gcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATAc         >  1:3007306/1‑62 (MQ=255)
                                                                  gcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTcaca  <  1:1696870/69‑1 (MQ=255)
                                                                    |                                                                  
TCCTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTCACA  >  minE/1826232‑1826366

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