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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,493,033 C→T 6.5% Q1072* (CAG→TAG)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,493,0330CT 6.5% 352.5 / 9.8 107Q1072* (CAG→TAG) evgShybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand):  ref base C (48/52);  new base T (5/2);  total (53/54)
Fisher's exact test for biased strand distribution p-value = 2.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

Only 100 of 112 total aligned reads displayed.

GTTAAGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAAATAATAC  >  W3110S.gb/2492963‑2493103
                                                                      |                                                                      
gTTAAGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTc                                                                        <  1:386714/71‑1 (MQ=255)
   aaGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGt                                                                     >  1:1088265/1‑71 (MQ=255)
     gTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTa                                                                   <  1:2106729/71‑1 (MQ=255)
     gTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTa                                                                   >  1:3379399/1‑71 (MQ=255)
       tGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTac                                                                  >  1:1100642/1‑70 (MQ=255)
        gCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTacac                                                                >  1:1176961/1‑71 (MQ=255)
        gCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTa                                                                   >  1:4119723/1‑68 (MQ=255)
         cGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACAcc                                                               <  1:3823712/71‑1 (MQ=255)
         cGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACAcc                                                               <  1:3543397/71‑1 (MQ=255)
         cGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACAcc                                                               <  1:612312/71‑1 (MQ=255)
          ggCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACAcc                                                               >  1:4252740/1‑70 (MQ=255)
            cATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCatg                                                            <  1:2161322/71‑3 (MQ=255)
             aTGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGt                                                           >  1:65827/1‑71 (MQ=255)
              tGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAg                                                            <  1:2065497/69‑1 (MQ=255)
              tGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGtt                                                          >  1:1014226/1‑71 (MQ=255)
                aaCTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTgc                                                        >  1:648237/1‑71 (MQ=255)
                   ttATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGt                                                                     <  1:531409/55‑1 (MQ=255)
                   ttATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCa                                                     >  1:85931/1‑71 (MQ=255)
                    tATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCa                                                     >  1:1038335/1‑70 (MQ=255)
                     aTGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCat                                                    <  1:1539234/70‑1 (MQ=255)
                      tgtttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTACACCAAGTTGCGCata                                                   >  1:2563998/1‑70 (MQ=255)
                       gtttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGt                                                                     >  1:666637/1‑51 (MQ=255)
                       gtttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGt                                                                     >  1:2482917/1‑51 (MQ=255)
                        tttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATAtt                                                 <  1:2641834/70‑1 (MQ=255)
                         ttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTACACCAAGTTGCGCATATTg                                                <  1:1955973/70‑1 (MQ=255)
                         ttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTACACCAAGTTGCGCATATTg                                                >  1:4058725/1‑70 (MQ=255)
                         ttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTACACCAAGTTGCGCATATTg                                                >  1:732548/1‑70 (MQ=255)
                         ttgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTg                                                >  1:4087637/1‑70 (MQ=255)
                          tgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAg                                                                      >  1:3248665/1‑47 (MQ=255)
                          tgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCa                                              >  1:3836766/1‑71 (MQ=255)
                          tgttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCa                                              >  1:789093/1‑71 (MQ=255)
                           gttCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCa                                              <  1:382205/70‑1 (MQ=255)
                              cAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCt                                           <  1:3000366/70‑1 (MQ=255)
                              cAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCt                                           >  1:2562265/1‑70 (MQ=255)
                               aaaCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTTAGTTACACCAAGTTGCGCATATTGCACCTc                                          <  1:305766/70‑1 (MQ=255)
                                aaCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAg                                        <  1:1480215/71‑1 (MQ=255)
                                aaCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAg                                        >  1:1441283/1‑71 (MQ=255)
                                aaCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAg                                        <  1:2167301/71‑1 (MQ=255)
                                 aCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTTCGCATATTGCACCTCa                                         >  1:3952334/1‑69 (MQ=255)
                                 aCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGt                                       <  1:3487426/71‑1 (MQ=255)
                                 aCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGt                                       <  1:3807491/71‑1 (MQ=255)
                                 aCCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGt                                       <  1:3360007/71‑1 (MQ=255)
                                  ccGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTac                                                                  >  1:888821/1‑43 (MQ=255)
                                  ccGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCa                                         >  1:1340310/1‑68 (MQ=255)
                                  ccGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTa                                      <  1:1513539/71‑1 (MQ=255)
                                     ttGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGt                                       <  1:573353/67‑1 (MQ=255)
                                     ttGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCg                                   <  1:1679280/71‑1 (MQ=255)
                                      tGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGc                                  >  1:216438/1‑71 (MQ=255)
                                        aCCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTgc                                                        <  1:3992119/47‑1 (MQ=255)
                                        aCCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTgc                                                        <  1:4178538/47‑1 (MQ=255)
                                        aCCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGcc                                 <  1:314650/70‑1 (MQ=255)
                                          ccTGGATGTACTGAAAACACATTTACGTCAGTTACACCAAGTTGCGCa                                                     <  1:4199467/48‑1 (MQ=255)
                                          ccTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCa                                                     <  1:4114838/48‑1 (MQ=255)
                                          ccTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCAcc                              >  1:3465375/1‑71 (MQ=255)
                                          ccTGCATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCAcc                              <  1:2455344/71‑1 (MQ=255)
                                           cTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATc                                    >  1:2708791/1‑64 (MQ=255)
                                           cTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCt                             <  1:3345208/71‑1 (MQ=255)
                                            tGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCa                                              >  1:3709708/1‑53 (MQ=255)
                                            tGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCAc                                             >  1:1894278/1‑54 (MQ=255)
                                            tGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGc                                  >  1:215241/1‑65 (MQ=255)
                                            tGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCt                             >  1:3393545/1‑70 (MQ=255)
                                             ggATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCtt                            >  1:887177/1‑70 (MQ=255)
                                             ggATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCt                             <  1:1321240/69‑1 (MQ=255)
                                             ggATGTACTGAAAACACATTTAAGTCAGTTACACCAAATTGCGCATATTGCAc                                             <  1:1749509/53‑1 (MQ=255)
                                              gATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCtt                            <  1:735618/69‑1 (MQ=255)
                                              gATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGa                          <  1:2848137/71‑1 (MQ=255)
                                                tGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACATTGata                        >  1:780858/1‑71 (MQ=255)
                                                 gTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCatat                                                  <  1:4491376/44‑1 (MQ=255)
                                                 gTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGatat                       >  1:2417216/1‑71 (MQ=255)
                                                  tACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCTCCACCTTGatat                       <  1:3937813/70‑1 (MQ=255)
                                                   aCTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATc                      >  1:1519012/1‑70 (MQ=255)
                                                    cTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATTTTGCACCTCAGTATCGCCACCtt                            <  1:4132359/63‑1 (MQ=255)
                                                    cTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCg                     <  1:3328856/70‑1 (MQ=255)
                                                     tGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGc                                               <  1:2990854/43‑1 (MQ=255)
                                                      gAAAACACATTTAAGTCAGTTACACCAAGTTGCGCa                                                     <  1:1236426/36‑1 (MQ=255)
                                                      gAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATc                                    >  1:4133653/1‑53 (MQ=255)
                                                      gAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCg                                   >  1:2820661/1‑54 (MQ=255)
                                                      gAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCg                                   >  1:1634849/1‑54 (MQ=255)
                                                       aaaaCACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGaa                   <  1:218868/69‑1 (MQ=255)
                                                       aaaaCACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGaa                   <  1:3720856/69‑1 (MQ=255)
                                                       aaaaCACATTTAAGACAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGaa                   >  1:2008574/1‑69 (MQ=255)
                                                          acacATTTAAGTCAGTTACACCAAGTTGCGCATATTg                                                <  1:705979/37‑1 (MQ=255)
                                                            acaTTTAAGTCAGTTACACCTAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAg                  <  1:3415133/65‑1 (MQ=255)
                                                            acaTTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCtt                            >  1:3550815/1‑55 (MQ=255)
                                                            acaTTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGcc                >  1:320495/1‑67 (MQ=255)
                                                            acaTTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTg             >  1:2376170/1‑70 (MQ=255)
                                                              aTTTAAGTTAGTTACACCAAGTTGCGCATATTGCAc                                             >  1:1717962/1‑36 (MQ=255)
                                                              aTTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGaaa          <  1:3387971/71‑1 (MQ=255)
                                                                ttAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGc                                  >  1:2381636/1‑45 (MQ=255)
                                                                ttAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGc                                  >  1:2386739/1‑45 (MQ=255)
                                                                 tAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCa                                         >  1:2853939/1‑37 (MQ=255)
                                                                 tAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGaaaaa        <  1:4509139/70‑1 (MQ=255)
                                                                 tAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGaaaaa        >  1:2874684/1‑70 (MQ=255)
                                                                  aaGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGatat                       >  1:3638225/1‑54 (MQ=255)
                                                                  aaGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGaa                   >  1:16397/1‑58 (MQ=255)
                                                                   aGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAaataa     <  1:268219/71‑1 (MQ=255)
                                                                    gTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCtt                            <  1:2781203/47‑1 (MQ=255)
                                                                      cAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGccc               >  1:3291596/1‑58 (MQ=255)
                                                                      cAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGccc               >  1:1760519/1‑58 (MQ=255)
                                                                      cAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAAATAATAc  >  1:1525443/1‑71 (MQ=255)
                                                                      |                                                                      
GTTAAGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAAATAATAC  >  W3110S.gb/2492963‑2493103

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