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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,192,465 C→T 45.0% D80N (GAT→AAT)  sspA ← stringent starvation protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,192,4650CT45.0% 29.6 / 104.2 80D80N (GAT→AAT) sspAstringent starvation protein A
Reads supporting (aligned to +/- strand):  ref base C (25/19);  new base T (16/20);  total (41/39)
Fisher's exact test for biased strand distribution p-value = 3.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01

CAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCT  >  minE/2192400‑2192533
                                                                 |                                                                    
cAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGa                                                                  <  1:1144077/70‑1 (MQ=255)
cAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGa                                                                  <  1:606474/70‑1 (MQ=255)
cAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGa                                                                  >  1:586317/1‑70 (MQ=255)
  gACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGatat                                                               >  1:3428655/1‑71 (MQ=255)
   aCGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGatat                                                               >  1:392337/1‑70 (MQ=255)
   aCGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATAtt                                                              >  1:4136782/1‑71 (MQ=255)
    cGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGa                                                                  >  1:114208/1‑66 (MQ=255)
    cGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTc                                                             <  1:1141403/71‑1 (MQ=255)
     ggCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTc                                                             >  1:2256066/1‑70 (MQ=255)
       cTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCAt                                                          <  1:13640/71‑1 (MQ=255)
         ttCACCGCGAGCTACCTGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATaa                                                        >  1:3362463/1‑71 (MQ=255)
         ttCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATaa                                                        >  1:1162037/1‑71 (MQ=255)
          tCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATaa                                                        <  1:2910694/70‑1 (MQ=255)
          tCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       >  1:1694111/1‑71 (MQ=255)
          tCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       >  1:882592/1‑71 (MQ=255)
           cACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAat                                                       <  1:1451303/70‑1 (MQ=255)
           cACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAat                                                       <  1:4002042/70‑1 (MQ=255)
            aCCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAatga                                                     >  1:801608/1‑71 (MQ=255)
             ccGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       <  1:3381376/68‑1 (MQ=255)
                cgAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCg                                                 <  1:1436560/71‑1 (MQ=255)
                cgAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGc                                                  <  1:2359559/70‑1 (MQ=255)
                 gAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCga                                                <  1:2956939/71‑1 (MQ=255)
                 gAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGc                                                  >  1:1340503/1‑69 (MQ=255)
                   gCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCa                                                           <  1:4062863/58‑1 (MQ=255)
                   gCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAat                                                       <  1:1799071/62‑1 (MQ=255)
                     tACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       <  1:2108328/60‑1 (MQ=255)
                      aCCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCa                                                                    >  1:964280/1‑46 (MQ=255)
                      aCCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTc                                                             >  1:2997221/1‑53 (MQ=255)
                      aCCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTc                                                             >  1:819694/1‑53 (MQ=255)
                      aCCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTc                                           >  1:266820/1‑71 (MQ=255)
                       ccGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCga                                                >  1:178006/1‑65 (MQ=255)
                       ccGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGAtt                                            <  1:2865639/69‑1 (MQ=255)
                       ccGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGAtt                                            <  1:2242744/69‑1 (MQ=255)
                         gggTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTccc                                         >  1:3068562/1‑70 (MQ=255)
                         gggTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCAt                                                          <  1:396206/53‑1 (MQ=255)
                         gggTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCca                                        <  1:3097378/71‑1 (MQ=255)
                         gggTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCca                                        <  1:2248263/71‑1 (MQ=255)
                            tAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTc                                                             <  1:1651973/47‑1 (MQ=255)
                             aaaCAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGata                                                                >  1:3749281/1‑43 (MQ=255)
                              aaCAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGa                                                                  >  1:1347991/1‑40 (MQ=255)
                              aaCAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcaca                                      >  1:25279/1‑68 (MQ=255)
                              aaCAGGCATCAGTGGAGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCca                                        >  1:4013560/1‑66 (MQ=255)
                                cAGGCATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       >  1:759851/1‑49 (MQ=255)
                                cAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGt                                  >  1:3094913/1‑70 (MQ=255)
                                    cATCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAat                                                       <  1:2491197/45‑1 (MQ=255)
                                    cATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCt                             <  1:780888/71‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTcc                                          <  1:1768536/56‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTcc                                          <  1:400107/56‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTcc                                          <  1:1311709/56‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGAt                                             <  1:2430349/53‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCt                             <  1:1038824/69‑1 (MQ=255)
                                      tCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGAGAGAt                                             <  1:1016619/53‑1 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                          >  1:591680/1‑70 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACg                         <  1:1098936/71‑1 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCgaga                                              >  1:706078/1‑50 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcaca                                      >  1:3482440/1‑58 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcaca                                      >  1:3487150/1‑58 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                          >  1:1626136/1‑70 (MQ=255)
                                        aGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACg                         <  1:3629189/71‑1 (MQ=255)
                                         gTGGCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGa                        <  1:3389584/71‑1 (MQ=255)
                                          tGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcaca                                      <  1:2880387/56‑1 (MQ=255)
                                           ggCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCg                                                 <  1:1534413/44‑1 (MQ=255)
                                            gCGGATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATc                      >  1:2650220/1‑70 (MQ=255)
                                               gATGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATccac                   <  1:3001013/70‑1 (MQ=255)
                                               gATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATccacc                  <  1:4136654/71‑1 (MQ=255)
                                                aTGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATccacca                 <  1:2519361/71‑1 (MQ=255)
                                                aTGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATccac                   >  1:3782290/1‑69 (MQ=255)
                                                 tGCGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAg                >  1:2525320/1‑71 (MQ=255)
                                                 tGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAg                >  1:122801/1‑71 (MQ=255)
                                                  gCGGGAAACGCTCATTCAGATATTCCATAatgatg                                                   >  1:2643449/1‑35 (MQ=255)
                                                  gCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAgg               >  1:273594/1‑71 (MQ=255)
                                                   cGGGAAACGCTCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAgg               <  1:1781020/70‑1 (MQ=255)
                                                      gAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAgg               >  1:134363/1‑67 (MQ=255)
                                                        aaCGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGc                              >  1:3976408/1‑50 (MQ=255)
                                                        aaCGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCa                           >  1:2810162/1‑53 (MQ=255)
                                                          cGCTCATCCAGATATTCCATAATGATGCGAGATTCCca                                        >  1:4076822/1‑38 (MQ=255)
                                                           gCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACg      <  1:2412725/71‑1 (MQ=255)
                                                             tCATTCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACg                         >  1:3108157/1‑50 (MQ=255)
                                                               aTCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGctct  >  1:2143606/1‑71 (MQ=255)
                                                               aTCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGctct  <  1:3995160/71‑1 (MQ=255)
                                                                 |                                                                    
CAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCT  >  minE/2192400‑2192533

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