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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 835,220 T→C 22.1% R1226R (CGT→CGC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2200TC22.1% 224.7 / 62.4 122R1226R (CGT→CGC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (45/50);  new base C (16/11);  total (61/61)
Fisher's exact test for biased strand distribution p-value = 3.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

Only 100 of 129 total aligned reads displayed.

CCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGAA  >  minE/835150‑835287
                                                                      |                                                                   
cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                                                     <  1:140015/71‑1 (MQ=255)
         cATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                                            <  1:3865259/71‑1 (MQ=255)
         cATACGGCTTTAACTACTATGGCACCGTAGGTCCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                                            <  1:3211259/71‑1 (MQ=255)
            ggggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAc                                                         >  1:4667421/3‑71 (MQ=255)
             cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                        >  1:5614683/1‑71 (MQ=255)
             cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                        <  1:442185/71‑1 (MQ=255)
              ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt                                                       <  1:2579900/71‑3 (MQ=255)
               gCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                      <  1:2893467/71‑1 (MQ=255)
                cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                      >  1:3862488/1‑70 (MQ=255)
                cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta                                                     <  1:3280931/71‑2 (MQ=255)
                    aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                                                  <  1:3100500/70‑1 (MQ=255)
                    aaCTACTACGGGACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                                                          >  1:5171552/1‑62 (MQ=255)
                    aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                                                          >  1:3456343/1‑62 (MQ=255)
                     actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt                                                       >  1:3442705/1‑64 (MQ=255)
                     actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                                <  1:4961804/71‑1 (MQ=255)
                      ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                                <  1:4001945/70‑1 (MQ=255)
                      ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                               <  1:105446/71‑1 (MQ=255)
                      ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                               <  1:3275169/71‑2 (MQ=255)
                         ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                               >  1:5368718/1‑68 (MQ=255)
                           acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAACAACGTTAACTGGCTGGAt                                          >  1:359637/3‑71 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                                             >  1:3205365/1‑51 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                                             >  1:1035745/1‑51 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                                             >  1:1552395/1‑51 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                        <  1:5095584/56‑1 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           <  1:1230388/69‑1 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           <  1:5171278/69‑1 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           <  1:1103606/69‑1 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                         >  1:5242741/1‑71 (MQ=255)
                            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                         >  1:1344664/1‑71 (MQ=255)
                            cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                                                    >  1:2452135/2‑58 (MQ=255)
                            cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                          <  1:3390824/69‑1 (MQ=255)
                            cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                          <  1:1590219/69‑1 (MQ=255)
                            cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                          <  1:4956914/69‑1 (MQ=255)
                            cggCACCGTCGGATCGAACCGCGATGAGCTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                          >  1:283218/2‑70 (MQ=255)
                             ggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                                        <  1:5684417/71‑2 (MQ=255)
                              gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                       >  1:3678124/1‑69 (MQ=255)
                              gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                       >  1:2619988/1‑69 (MQ=255)
                              gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                       >  1:227615/1‑69 (MQ=255)
                              gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                                        >  1:5190126/1‑69 (MQ=255)
                              gCACCGTCGGATCGAACCGCGATGACTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                       <  1:733046/71‑3 (MQ=255)
                              gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGAc                                                   >  1:3683516/1‑59 (MQ=255)
                              gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg                                        <  1:5209487/70‑1 (MQ=255)
                               cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGTAGAACATTGACTGGTTAGATGGCg                                      <  1:2297451/71‑1 (MQ=255)
                               cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                            >  1:5296291/1‑65 (MQ=255)
                               cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                            >  1:1898385/1‑65 (MQ=255)
                               cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                      <  1:2319062/71‑1 (MQ=255)
                               cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                      <  1:2292372/71‑1 (MQ=255)
                                aCCGTAGGTTGTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                      <  1:4327716/70‑1 (MQ=255)
                                 ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                      >  1:2935844/1‑69 (MQ=255)
                                  cGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                <  1:3136321/58‑1 (MQ=255)
                                   gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                                                 >  1:4806926/1‑40 (MQ=255)
                                   gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                                                 >  1:1300459/1‑40 (MQ=255)
                                   gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGGAGAACATTGACTGGTTa                                             >  1:2039359/1‑60 (MQ=255)
                                   gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                             >  1:1116169/1‑60 (MQ=255)
                                   gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAgg                                  >  1:932341/1‑71 (MQ=255)
                                    tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                        >  1:3197425/1‑48 (MQ=255)
                                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                      <  1:30916/47‑1 (MQ=255)
                                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                             <  1:1946457/56‑1 (MQ=255)
                                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                             <  1:5485123/56‑1 (MQ=255)
                                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                              <  1:959522/71‑1 (MQ=255)
                                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                              <  1:4239680/71‑1 (MQ=255)
                                         tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           >  1:4934101/1‑56 (MQ=255)
                                         tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                                       <  1:1346366/60‑1 (MQ=255)
                                         tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                            >  1:785147/1‑71 (MQ=255)
                                          cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           >  1:2503013/1‑71 (MQ=255)
                                          cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           >  1:340032/1‑71 (MQ=255)
                                           tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                             <  1:628252/52‑1 (MQ=255)
                                           tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                             <  1:4870463/52‑1 (MQ=255)
                                           tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           >  1:4231039/1‑70 (MQ=255)
                                            aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           >  1:5509325/1‑69 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           <  1:4227824/52‑1 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                            <  1:2149009/67‑1 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAcc                          <  1:5054707/69‑1 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           <  1:1694742/68‑1 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           <  1:1877255/68‑1 (MQ=255)
                                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                           <  1:4592101/68‑1 (MQ=255)
                                             aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                   >  1:657043/1‑44 (MQ=255)
                                             aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                   >  1:3547809/1‑44 (MQ=255)
                                              ccGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATg                                         <  1:2007834/53‑1 (MQ=255)
                                                gcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                     >  1:2143009/1‑71 (MQ=255)
                                                 cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                     >  1:3728797/1‑70 (MQ=255)
                                                 cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                    <  1:2486915/71‑1 (MQ=255)
                                                  gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                     >  1:5679238/1‑69 (MQ=255)
                                                         ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                           <  1:1614334/40‑1 (MQ=255)
                                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                            >  1:786608/1‑38 (MQ=255)
                                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                            >  1:5434985/1‑38 (MQ=255)
                                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                          >  1:4855383/1‑40 (MQ=255)
                                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                               >  1:4375949/1‑51 (MQ=255)
                                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg           >  1:3439300/1‑71 (MQ=255)
                                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                          >  1:4466483/1‑36 (MQ=255)
                                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                          >  1:3267547/1‑36 (MQ=255)
                                                               tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaaaa      <  1:3577390/71‑1 (MQ=255)
                                                                 gTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                    >  1:4810196/1‑39 (MQ=255)
                                                                  tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGa   <  1:2664627/71‑1 (MQ=255)
                                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaaaa      >  1:4523821/1‑66 (MQ=255)
                                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGaa  <  1:5539812/70‑1 (MQ=255)
                                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGaa  <  1:2785236/70‑1 (MQ=255)
                                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGaa  >  1:3055297/1‑70 (MQ=255)
                                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGaa  >  1:839110/1‑70 (MQ=255)
                                                                      tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                         >  1:1141528/1‑45 (MQ=255)
                                                                      |                                                                   
CCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGAA  >  minE/835150‑835287

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