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 1,933,312 T→A 18.2% E377D (GAA→GAT)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,3120TA18.2% 173.4 / 33.4 77E377D (GAA→GAT) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base T (29/34);  new base A (8/6);  total (37/40)
Fisher's exact test for biased strand distribution p-value = 5.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

CAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCA  >  minE/1933243‑1933381
                                                                     |                                                                     
cAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtctt                                                                      >  1:3056262/1‑71 (MQ=255)
cAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtctt                                                                      >  1:1575206/1‑71 (MQ=255)
cAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtctt                                                                      <  1:1288964/71‑1 (MQ=255)
cAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtctt                                                                      <  1:2490657/71‑1 (MQ=255)
 aGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACttcttc                                                                     <  1:2505579/71‑1 (MQ=255)
  gCGGGGACACTTCTGCCGTATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatca                                                                    <  1:1798835/71‑2 (MQ=255)
  gCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatca                                                                    <  1:1455906/71‑2 (MQ=255)
  gCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatc                                                                     >  1:2304842/1‑70 (MQ=255)
  gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACttcttc                                                                     >  1:3209953/1‑70 (MQ=255)
  gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                                                                    <  1:2743481/71‑1 (MQ=255)
  gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                                                                    <  1:1282024/71‑1 (MQ=255)
   cGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGa                                                                   <  1:3332325/71‑1 (MQ=255)
         aaCTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtct                                                             <  1:3191140/71‑1 (MQ=255)
           cTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                                                                    <  1:1180128/62‑1 (MQ=255)
           cTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCg                                                           <  1:677601/71‑1 (MQ=255)
            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatc                                                                     >  1:3214535/1‑60 (MQ=255)
            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctctg                                                          >  1:3427040/1‑69 (MQ=255)
            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctctg                                                          >  1:1462838/1‑69 (MQ=255)
            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctctg                                                          >  1:1793457/1‑69 (MQ=255)
            ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCgg                                                          >  1:546764/1‑71 (MQ=255)
              cTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGt                                                         >  1:1528363/1‑70 (MQ=255)
              cTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGt                                                         <  1:3167784/70‑1 (MQ=255)
              cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                                                         >  1:324878/1‑70 (MQ=255)
               tGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTaa                                                       >  1:1404275/1‑71 (MQ=255)
                gCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtct                                                                       >  1:1932959/1‑54 (MQ=255)
                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTa                                                        <  1:2387211/68‑1 (MQ=255)
                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTa                                                        <  1:1810719/68‑1 (MQ=255)
                  cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAca                                                     <  1:2562765/70‑2 (MQ=255)
                  cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAc                                                      <  1:3765587/69‑1 (MQ=255)
                  cGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGACACTTCTTCGAAGATCTCGGTAACGa                                                    >  1:831199/1‑71 (MQ=255)
                   ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGa                                                                <  1:2126397/58‑1 (MQ=255)
                   ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                    >  1:3495522/1‑70 (MQ=255)
                   ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                    >  1:1592644/1‑70 (MQ=255)
                    gATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                  <  1:3900767/71‑1 (MQ=255)
                      tatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACg                                                >  1:436776/1‑71 (MQ=255)
                         tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtctc                                                            <  1:2358898/56‑1 (MQ=255)
                         tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                             >  1:3371050/1‑71 (MQ=255)
                          ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATa                                                  >  1:489336/3‑65 (MQ=255)
                          cAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                    >  1:1451068/1‑63 (MQ=255)
                           cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatc                                                                     <  1:2671391/44‑1 (MQ=255)
                             tAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                                                                    <  1:3327095/44‑1 (MQ=255)
                              aaTAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCaacc                                        >  1:522311/1‑68 (MQ=255)
                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                      <  1:3098484/71‑1 (MQ=255)
                                 gAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                      >  1:2327411/1‑70 (MQ=255)
                                 gAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                      >  1:2167486/1‑70 (MQ=255)
                                  aaGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGtga                                                       <  1:1770045/52‑3 (MQ=255)
                                  aaGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCA‑Acccc                                     >  1:815524/1‑69 (MQ=255)
                                  aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcccc                                     <  1:3802313/70‑1 (MQ=255)
                                   aGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCg                                                           >  1:783357/1‑47 (MQ=255)
                                   aGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCg                                                           >  1:1087968/1‑47 (MQ=255)
                                     gTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtct                                                             <  1:2675862/43‑1 (MQ=255)
                                      ttggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGctt                                <  1:3338806/69‑2 (MQ=255)
                                             aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                           <  1:2603798/69‑1 (MQ=255)
                                             aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                           <  1:854070/69‑1 (MQ=255)
                                             aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                          <  1:999637/70‑1 (MQ=255)
                                             aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                          <  1:2218973/70‑1 (MQ=255)
                                              aTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAAc                        <  1:2021833/71‑1 (MQ=255)
                                               tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGct                                 <  1:1377821/61‑1 (MQ=255)
                                               tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACg                       <  1:952308/71‑1 (MQ=255)
                                               tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACg                       <  1:934048/71‑1 (MQ=255)
                                                cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCaa                         >  1:1336831/1‑68 (MQ=255)
                                                 aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAg                                   >  1:2657762/1‑57 (MQ=255)
                                                 aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGctct                               >  1:958536/1‑61 (MQ=255)
                                                 aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGt                      <  1:1039940/70‑1 (MQ=255)
                                                 aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTg                     >  1:634405/1‑71 (MQ=255)
                                                 aGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAccg                      <  1:3288293/70‑3 (MQ=255)
                                                   aTGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                             <  1:91851/45‑1 (MQ=255)
                                                     gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                    >  1:1051086/1‑36 (MQ=255)
                                                     gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                   <  1:3281668/37‑1 (MQ=255)
                                                     gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                 >  1:3084274/1‑71 (MQ=255)
                                                     gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                 >  1:3077592/1‑71 (MQ=255)
                                                        cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGTCCCAGACCCCAGCTCTTCTCAACGTGGATGCCg              <  1:2445001/71‑1 (MQ=255)
                                                        cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc               >  1:830991/1‑70 (MQ=255)
                                                        cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCg              <  1:2270213/71‑1 (MQ=255)
                                                         ttCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                      >  1:2435912/1‑46 (MQ=255)
                                                          tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGa             >  1:3042568/1‑70 (MQ=255)
                                                          tCTGCCACTTATTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                       >  1:136297/1‑44 (MQ=255)
                                                           cTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtctt                              >  1:12180/1‑52 (MQ=255)
                                                           cTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGa             >  1:375866/1‑69 (MQ=255)
                                                             gCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTg                     >  1:644045/1‑59 (MQ=255)
                                                              ccACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                           <  1:755818/52‑1 (MQ=255)
                                                              ccACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                           <  1:1017272/52‑1 (MQ=255)
                                                              ccACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCg              <  1:398359/65‑1 (MQ=255)
                                                              ccACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAg          <  1:2631763/69‑1 (MQ=255)
                                                              ccACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAt        <  1:3622973/71‑1 (MQ=255)
                                                               cACTTCTTCGAAGATCTCGGTAACTATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt       <  1:2911318/71‑1 (MQ=255)
                                                               cACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAAc                        >  1:899521/1‑54 (MQ=255)
                                                               cACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGa             >  1:1345345/1‑65 (MQ=255)
                                                                aCTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt       >  1:2278324/1‑70 (MQ=255)
                                                                 cttcttCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAAc                        >  1:3102110/1‑52 (MQ=255)
                                                                    cttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAt        <  1:1293342/65‑1 (MQ=255)
                                                                    cttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGc   >  1:1524940/1‑70 (MQ=255)
                                                                     ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGa         <  1:2562539/63‑1 (MQ=255)
                                                                     ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCa  >  1:1968865/1‑70 (MQ=255)
                                                                     |                                                                     
CAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCA  >  minE/1933243‑1933381

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