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 835,220 T→C 13.5% 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
*minE835,2200TC13.5% 240.9 / 26.3 96R1226R (CGT→CGC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (41/42);  new base C (9/4);  total (50/46)
Fisher's exact test for biased strand distribution p-value = 2.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

CCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGAAAAT  >  minE/835151‑835290
                                                                     |                                                                      
ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTa                                                                       <  1:1495627/71‑1 (MQ=255)
  aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                                                        >  1:470160/1‑68 (MQ=255)
       gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATg                                                                  <  1:3848771/69‑1 (MQ=255)
          tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                                                             >  1:3157522/1‑71 (MQ=255)
          tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                              >  1:2413535/1‑70 (MQ=255)
           aCGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                                                             >  1:2662020/1‑70 (MQ=255)
            cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                                                            <  1:1441248/70‑1 (MQ=255)
            cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                           >  1:3578172/1‑71 (MQ=255)
             ggCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                           >  1:1272169/1‑70 (MQ=255)
             ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt                                                          >  1:1695585/1‑69 (MQ=255)
               cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                         >  1:2849592/1‑70 (MQ=255)
               cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                         >  1:3558716/1‑70 (MQ=255)
               cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                                        <  1:3580214/71‑1 (MQ=255)
               cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                                        <  1:1633377/71‑1 (MQ=255)
               cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta                                                        <  1:297796/71‑2 (MQ=255)
                 ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                      >  1:2657265/1‑71 (MQ=255)
                 ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                      >  1:2248875/1‑71 (MQ=255)
                 ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                      >  1:110190/1‑71 (MQ=255)
                  tAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACt                                                     >  1:3348933/1‑71 (MQ=255)
                   aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                    >  1:48316/1‑71 (MQ=255)
                    actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcg                                                           <  1:1522885/63‑2 (MQ=255)
                    actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                   >  1:1627332/1‑71 (MQ=255)
                    actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                   <  1:914913/71‑1 (MQ=255)
                     ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                                  >  1:3641095/1‑70 (MQ=255)
                        ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                <  1:1907475/70‑1 (MQ=255)
                        ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                <  1:2382585/70‑1 (MQ=255)
                        ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                <  1:3220800/70‑1 (MQ=255)
                        ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                <  1:3456589/70‑1 (MQ=255)
                        ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                                <  1:1429012/70‑4 (MQ=255)
                        ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                                >  1:2086464/1‑67 (MQ=255)
                          acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                             >  1:2152391/3‑71 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                                                            >  1:3636905/1‑55 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                       >  1:2879013/1‑60 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                       >  1:3271910/1‑60 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                       >  1:1677448/1‑60 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                       >  1:543449/1‑60 (MQ=255)
                           tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                             <  1:1095397/70‑1 (MQ=255)
                             gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATg                                                                  >  1:3240278/1‑47 (MQ=255)
                              cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGAt                                                                   <  1:1714743/45‑1 (MQ=255)
                                ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAGGAACATTGACTGGTTAGATGGCGaa                                       <  1:487614/71‑1 (MQ=255)
                                ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                           <  1:3599427/51‑1 (MQ=255)
                                ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                       <  1:725893/71‑1 (MQ=255)
                                   tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGc                                    <  1:464788/71‑1 (MQ=255)
                                      gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                  <  1:1175320/54‑1 (MQ=255)
                                       ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                                                             <  1:1097543/42‑1 (MQ=255)
                                       ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATg                                <  1:1214518/71‑1 (MQ=255)
                                        tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                            >  1:1144809/1‑58 (MQ=255)
                                          tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                 >  1:82640/1‑67 (MQ=255)
                                           aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                              >  1:2092632/1‑37 (MQ=255)
                                           aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                              >  1:417241/1‑37 (MQ=255)
                                           aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                 <  1:2957897/66‑1 (MQ=255)
                                            aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                         <  1:1961004/41‑1 (MQ=255)
                                            aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                         <  1:701564/41‑1 (MQ=255)
                                            aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                         <  1:645685/41‑1 (MQ=255)
                                            aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                            >  1:2595832/1‑54 (MQ=255)
                                            aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                            <  1:2070912/54‑1 (MQ=255)
                                            aCCGAGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                 >  1:2624426/1‑65 (MQ=255)
                                             ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                 >  1:1615579/1‑64 (MQ=255)
                                             ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAg                           <  1:3194256/70‑1 (MQ=255)
                                              cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                    >  1:3157168/1‑44 (MQ=255)
                                              cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGt                         <  1:3802636/71‑1 (MQ=255)
                                                 gatgatTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACa                      <  1:652433/71‑1 (MQ=255)
                                                 gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                        <  1:3274004/53‑1 (MQ=255)
                                                 gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                        <  1:3853295/53‑1 (MQ=255)
                                                 gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                        <  1:370518/53‑1 (MQ=255)
                                                  aTGAGTTTGTTGTAGTGTGTAAGATGAAGAACATTGACTg                                                    <  1:251812/40‑1 (MQ=255)
                                                  aTGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                     <  1:853548/71‑1 (MQ=255)
                                                    gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                  >  1:1693123/1‑40 (MQ=255)
                                                    gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                  >  1:1997888/1‑40 (MQ=255)
                                                    gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                     >  1:959944/1‑69 (MQ=255)
                                                     aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                  >  1:3146941/1‑55 (MQ=255)
                                                     aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga                   <  1:1839570/70‑1 (MQ=255)
                                                     aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga                   <  1:3819905/70‑1 (MQ=255)
                                                        ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga                 >  1:780615/1‑69 (MQ=255)
                                                        ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga                 >  1:2702740/1‑69 (MQ=255)
                                                         tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                                 <  1:3509032/36‑1 (MQ=255)
                                                         tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                                 <  1:3228479/36‑1 (MQ=255)
                                                         tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                       >  1:3896716/1‑46 (MQ=255)
                                                         tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg              >  1:541158/1‑71 (MQ=255)
                                                          gttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg              >  1:3855325/1‑70 (MQ=255)
                                                            tgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                     >  1:3705822/1‑61 (MQ=255)
                                                            tgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTa            >  1:3829155/1‑70 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                              >  1:294759/1‑35 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                             >  1:79511/1‑36 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                     >  1:1157715/1‑60 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaa           >  1:3759474/1‑70 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaa           <  1:2938315/70‑1 (MQ=255)
                                                             gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaa           >  1:328648/1‑70 (MQ=255)
                                                              tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                            <  1:3943261/52‑1 (MQ=255)
                                                              tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                            <  1:1170022/52‑1 (MQ=255)
                                                              tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaaa          <  1:3301694/70‑1 (MQ=255)
                                                               aGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTaaaa         <  1:2017284/70‑1 (MQ=255)
                                                               aGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAAt        >  1:3537989/1‑71 (MQ=255)
                                                                 tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                       <  1:3371468/54‑1 (MQ=255)
                                                                 tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                       <  1:504547/54‑1 (MQ=255)
                                                                  gCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGa      >  1:2445047/1‑70 (MQ=255)
                                                                   cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAg                                      >  1:2462320/1‑37 (MQ=255)
                                                                     tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGa      <  1:3772670/67‑1 (MQ=255)
                                                                     tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGAAAAt  <  1:751456/71‑1 (MQ=255)
                                                                     tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGAGTAAAATGAAAAt  <  1:3862461/71‑1 (MQ=255)
                                                                     |                                                                      
CCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCGTAAAATGAAAAT  >  minE/835151‑835290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A