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
A3 F8 I0 R2 41 28.0 2221522 97.3% 2161540 59.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 59.0% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,809,5810GA59.0% 46.2 / 105.6 83G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (20/14);  new base A (24/25);  total (44/39)
Fisher's exact test for biased strand distribution p-value = 5.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTC  >  W3110S.gb/2809517‑2809649
                                                                |                                                                    
gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                <  1:1155367/71‑1 (MQ=255)
 tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                >  1:2013385/1‑70 (MQ=255)
 tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                               <  1:1695458/71‑1 (MQ=255)
   tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                >  1:2021721/1‑68 (MQ=255)
   tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                >  1:2164260/1‑68 (MQ=255)
     tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                           >  1:410619/1‑71 (MQ=255)
      gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                              <  1:796215/67‑1 (MQ=255)
       catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                         <  1:1974532/71‑1 (MQ=255)
       catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                         <  1:479163/71‑1 (MQ=255)
         tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                   <  1:766515/59‑1 (MQ=255)
         tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                   <  1:1748551/59‑1 (MQ=255)
          gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                      >  1:1699801/1‑71 (MQ=255)
          gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                      >  1:642877/1‑71 (MQ=255)
           cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                     >  1:316028/1‑55 (MQ=255)
           cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                      <  1:1697555/70‑1 (MQ=255)
           cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                     <  1:501294/71‑1 (MQ=255)
              atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                 >  1:492732/1‑56 (MQ=255)
               tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                 >  1:1207114/1‑71 (MQ=255)
               tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                   <  1:316551/53‑1 (MQ=255)
               tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                   <  1:104890/53‑1 (MQ=255)
                gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                <  1:809667/55‑1 (MQ=255)
                gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                >  1:2117259/1‑71 (MQ=255)
                 caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                               <  1:144885/71‑1 (MQ=255)
                 caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                   <  1:1448758/51‑1 (MQ=255)
                 caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                   >  1:1192335/1‑67 (MQ=255)
                    agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                 >  1:937619/1‑50 (MQ=255)
                    agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                     >  1:265030/1‑62 (MQ=255)
                    agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                            <  1:1534007/71‑1 (MQ=255)
                     gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                            >  1:2020618/1‑70 (MQ=255)
                      caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                     >  1:1000592/1‑44 (MQ=255)
                      caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                          <  1:1221092/71‑1 (MQ=255)
                       aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                <  1:1188160/48‑1 (MQ=255)
                       aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                         <  1:1468833/71‑1 (MQ=255)
                       aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                         <  1:1471491/71‑1 (MQ=255)
                        agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:1530330/1‑69 (MQ=255)
                         gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                 <  1:1088943/45‑1 (MQ=255)
                          ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                      >  1:1141243/1‑71 (MQ=255)
                              tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                   <  1:247349/38‑1 (MQ=255)
                               ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                  >  1:894498/1‑70 (MQ=255)
                               ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                      <  1:1451861/50‑1 (MQ=255)
                                gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                      >  1:1716407/1‑49 (MQ=255)
                                gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:870565/1‑61 (MQ=255)
                                     ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                           >  1:834274/1‑55 (MQ=255)
                                     ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                           <  1:588319/71‑1 (MQ=255)
                                     ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                           <  1:1092594/71‑1 (MQ=255)
                                     ccGCAATAAAATGCTGAAGGCTCAGGGAAATAACGAGACGTTGTTTATGGCGTTGATTa                                       >  1:1436239/1‑59 (MQ=255)
                                      cGCACTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                              <  1:1850977/67‑1 (MQ=255)
                                      cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                              <  1:1973258/67‑1 (MQ=255)
                                       gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                 >  1:1882941/1‑47 (MQ=255)
                                       gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:445763/1‑54 (MQ=255)
                                       gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:1315818/1‑54 (MQ=255)
                                       gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                         >  1:376316/1‑71 (MQ=255)
                                       gCAATAAAAAGCTGAAGGCTCAGGGGATTAACGAGACgt                                                         >  1:150417/1‑39 (MQ=255)
                                        cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                >  1:1518495/1‑63 (MQ=255)
                                          aTAAAATGCTTAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                      <  1:1195782/71‑1 (MQ=255)
                                          aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                  <  1:1167331/43‑1 (MQ=255)
                                           tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                    <  1:637092/40‑1 (MQ=255)
                                           tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                      <  1:1410285/70‑1 (MQ=255)
                                            aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                    >  1:1718333/1‑71 (MQ=255)
                                            aaaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                     >  1:1260354/1‑38 (MQ=255)
                                            aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                   >  1:1032040/1‑40 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                     >  1:720091/1‑37 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:1454587/1‑48 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                 >  1:268077/1‑57 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                   >  1:1776450/1‑39 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                       >  1:1591133/1‑51 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                       >  1:1931023/1‑51 (MQ=255)
                                             aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                >  1:669306/1‑58 (MQ=255)
                                              aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                  <  1:2085363/71‑1 (MQ=255)
                                               aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                              >  1:558489/1‑42 (MQ=255)
                                               aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                 <  1:147827/71‑1 (MQ=255)
                                                  cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg              >  1:1937196/1‑71 (MQ=255)
                                                   tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                         <  1:820888/43‑1 (MQ=255)
                                                    gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                            <  1:1207498/55‑1 (MQ=255)
                                                     aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                          >  1:2220282/1‑40 (MQ=255)
                                                     aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                            <  1:1022936/54‑1 (MQ=255)
                                                     aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                >  1:1255061/1‑66 (MQ=255)
                                                        gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                     <  1:810839/42‑1 (MQ=255)
                                                        gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa        <  1:2093978/71‑1 (MQ=255)
                                                        gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa        <  1:917400/71‑1 (MQ=255)
                                                            aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                       >  1:1910472/1‑36 (MQ=255)
                                                            aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg              <  1:1527275/61‑1 (MQ=255)
                                                            aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt    >  1:1719978/1‑71 (MQ=255)
                                                              gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTc  >  1:2069844/1‑71 (MQ=255)
                                                                |                                                                    
GTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTC  >  W3110S.gb/2809517‑2809649

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