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 F21 I0 R1 148 22.8 1772010 97.0% 1718849 61.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 61.5% 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.gb2,809,5810GA61.5% 48.2 / 72.9 65G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (17/8);  new base A (14/26);  total (31/34)
Fisher's exact test for biased strand distribution p-value = 1.19e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATT  >  W3110S.gb/2809515‑2809641
                                                                  |                                                            
tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGTGAtt                                                           >  1:698128/1‑70 (MQ=255)
  gTCTTTGCATGCACGTGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                          <  1:1469274/69‑1 (MQ=255)
  gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                          <  1:238057/69‑1 (MQ=255)
  gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                          <  1:980202/69‑1 (MQ=255)
   tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                       <  1:544714/71‑1 (MQ=255)
   tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                       <  1:146899/71‑1 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                        >  1:1676520/1‑68 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                           <  1:1199793/65‑1 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                        >  1:737422/1‑68 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                     <  1:1701434/69‑1 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                      <  1:1248719/68‑1 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                      <  1:1635291/68‑1 (MQ=255)
        gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                  >  1:656540/1‑71 (MQ=255)
         catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                  <  1:1062192/70‑1 (MQ=255)
           tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                               <  1:372133/71‑1 (MQ=255)
             tgcatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                             >  1:1190460/3‑71 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCATTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                             <  1:66834/71‑1 (MQ=255)
              acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                             >  1:419955/1‑70 (MQ=255)
              acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                            <  1:131333/71‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                          >  1:1364627/1‑71 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                          <  1:164831/71‑1 (MQ=255)
                 tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                            <  1:549978/68‑1 (MQ=255)
                 tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                           <  1:1733953/53‑1 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                        >  1:1241007/1‑71 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                       >  1:1328703/1‑71 (MQ=255)
                    aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                 >  1:726271/1‑60 (MQ=255)
                      agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                    <  1:598178/71‑1 (MQ=255)
                       gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                    <  1:1247631/70‑1 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                 <  1:1379612/71‑1 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                 <  1:323685/71‑1 (MQ=255)
                          agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                 >  1:1585670/1‑70 (MQ=255)
                           gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                           <  1:128641/43‑1 (MQ=255)
                           gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                             <  1:1579601/57‑1 (MQ=255)
                            ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAc                              >  1:484227/1‑71 (MQ=255)
                            ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                           <  1:640873/42‑1 (MQ=255)
                              gctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                             <  1:615330/38‑1 (MQ=255)
                                tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                     >  1:157123/1‑44 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                          <  1:325947/69‑1 (MQ=255)
                                   agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                       >  1:1084572/1‑71 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                        >  1:937809/1‑37 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                        >  1:560184/1‑37 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                               <  1:1418037/62‑1 (MQ=255)
                                      aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                    <  1:698932/71‑1 (MQ=255)
                                       ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGt                                     >  1:1653503/1‑53 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa              <  1:160440/71‑1 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa              >  1:1081647/1‑70 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa              >  1:112165/1‑70 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa              >  1:534582/1‑70 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                <  1:1239716/36‑1 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa              >  1:867940/1‑70 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTTGAGTCTCAGGAAAAc           >  1:1451802/1‑71 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                           >  1:1405073/1‑39 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                     >  1:425140/1‑45 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                           >  1:1679419/1‑37 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                           >  1:1359770/1‑37 (MQ=255)
                                                  tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                           >  1:1664246/1‑36 (MQ=255)
                                                  tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                                <  1:1259498/47‑1 (MQ=255)
                                                  tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                                <  1:1136439/47‑1 (MQ=255)
                                                    cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                 >  1:736029/1‑60 (MQ=255)
                                                      gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa    >  1:574683/1‑71 (MQ=255)
                                                       aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt   <  1:608622/71‑1 (MQ=255)
                                                        aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt  <  1:1277322/71‑1 (MQ=255)
                                                             cAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca       <  1:478699/61‑1 (MQ=255)
                                                              aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac        >  1:1739801/1‑59 (MQ=255)
                                                              aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCACAGGAAAACcac        >  1:974305/1‑59 (MQ=255)
                                                               gggaATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                          <  1:656408/40‑1 (MQ=255)
                                                                  |                                                            
TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATT  >  W3110S.gb/2809515‑2809641

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