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
A46 F1 I1 R1 17 71.0 4433184 98.0% 4344520 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,367,985 C→T R317H (CGC→CAC)  rpoA ← DNA‑directed RNA polymerase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,367,9850CT98.8% 301.2 / ‑4.5 81R317H (CGC→CAC) rpoADNA‑directed RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (40/40);  total (41/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

CCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAG  >  REL606/3367913‑3368057
                                                                        |                                                                        
ccTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCa                                                                       >  1:894139/1‑76 (MQ=255)
 cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCAt                                                                      >  2:620983/1‑76 (MQ=255)
 cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCAt                                                                      <  1:1790169/76‑1 (MQ=255)
 cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCAt                                                                      >  1:187855/1‑76 (MQ=255)
   tctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGc                                                                    >  1:499325/1‑76 (MQ=255)
   tctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGc                                                                    <  1:1577604/76‑1 (MQ=255)
   tctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGGGGCCAGTTTTCCAGGTGCATGc                                                                    >  1:499298/1‑76 (MQ=255)
    ctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGcc                                                                   >  1:2088918/1‑76 (MQ=255)
      cAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCa                                                                 >  2:138478/1‑76 (MQ=255)
       aGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCag                                                                <  2:1189298/76‑1 (MQ=255)
        gTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCaga                                                               <  1:1835640/76‑1 (MQ=255)
         tAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCagag                                                              <  1:139299/76‑1 (MQ=255)
          aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAgaga                                                             >  2:221102/1‑76 (MQ=255)
          aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAgaga                                                             >  2:223472/1‑76 (MQ=255)
           aaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGAc                                                            <  2:148895/76‑1 (MQ=255)
             aCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAg                                                          >  1:1740693/1‑76 (MQ=255)
             aCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAg                                                          <  2:877931/76‑1 (MQ=255)
              ccTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGt                                                         >  1:1832894/1‑76 (MQ=255)
               cTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTc                                                        >  1:1506305/1‑76 (MQ=255)
                ttAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTcc                                                       <  2:1689034/76‑1 (MQ=255)
                 tAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCa                                                      >  2:441772/1‑76 (MQ=255)
                 tAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCa                                                      <  2:528814/76‑1 (MQ=255)
                 tAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCa                                                      >  1:1679847/1‑76 (MQ=255)
                  aaCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCAc                                                     <  2:1964186/76‑1 (MQ=255)
                  aaCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCAc                                                     >  2:1409838/1‑76 (MQ=255)
                  aaCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCAc                                                     >  2:1312854/1‑76 (MQ=255)
                  aaCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCAc                                                     >  2:578203/1‑76 (MQ=255)
                   aCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACg                                                    <  2:80511/76‑1 (MQ=255)
                    ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACgg                                                   <  1:376591/76‑1 (MQ=255)
                     cTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACggg                                                  >  1:249961/1‑76 (MQ=255)
                      tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGa                                                 >  1:211238/1‑76 (MQ=255)
                      tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGa                                                 <  2:1234228/76‑1 (MQ=255)
                       gtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGaa                                                <  2:912774/76‑1 (MQ=255)
                       gtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGaa                                                <  2:124967/76‑1 (MQ=255)
                        tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAg                                               <  2:746298/76‑1 (MQ=255)
                        tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAg                                               >  2:2132310/1‑76 (MQ=255)
                        tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAg                                               >  2:1490245/1‑76 (MQ=255)
                         gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGc                                              >  2:1068394/1‑76 (MQ=255)
                         gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGc                                              >  2:429728/1‑76 (MQ=255)
                          aTCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGcc                                             >  2:1961517/1‑76 (MQ=255)
                          aTCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGcc                                             <  1:1071899/76‑1 (MQ=255)
                          aTCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGcc                                             >  1:570249/1‑76 (MQ=255)
                            ccGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAg                                           >  2:763402/1‑76 (MQ=255)
                            ccGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAg                                           >  1:130793/1‑76 (MQ=255)
                            ccGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAg                                           >  1:1942882/1‑76 (MQ=255)
                              ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCa                                         <  1:156568/76‑1 (MQ=255)
                               gTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCAc                                        >  1:1902982/1‑76 (MQ=255)
                                ttACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACg                                       <  2:1898455/76‑1 (MQ=255)
                                  aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                                     >  1:1927178/1‑76 (MQ=255)
                                   cTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCt                                    >  2:1751241/1‑76 (MQ=255)
                                     cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCttt                                  >  1:319260/1‑76 (MQ=255)
                                      gTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTa                                 <  1:1065768/76‑1 (MQ=255)
                                       tCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTaa                                <  2:256809/76‑1 (MQ=255)
                                       tCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTaa                                <  1:144468/76‑1 (MQ=255)
                                       tCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTaa                                <  1:421573/76‑1 (MQ=255)
                                        cAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAt                               >  1:719595/1‑76 (MQ=255)
                                         aGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAtc                              <  1:1682608/76‑1 (MQ=255)
                                         aGCGATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAtc                              >  2:2082940/1‑76 (MQ=255)
                                            gATGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCa                           <  1:845832/76‑1 (MQ=255)
                                              tGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGt                         <  1:1449239/76‑1 (MQ=255)
                                              tGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGt                         <  1:1255611/76‑1 (MQ=255)
                                              tGCTTGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGt                         <  1:580446/76‑1 (MQ=255)
                                                 ttGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAag                      <  1:1893053/76‑1 (MQ=255)
                                                 ttGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAag                      >  2:311731/1‑76 (MQ=255)
                                                 ttGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTGAATCTCAGTAag                      >  2:469982/1‑76 (MQ=255)
                                                  tGCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAaga                     >  2:2213229/1‑76 (MQ=255)
                                                   gCCGGTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAagag                    <  1:1967261/76‑1 (MQ=255)
                                                      ggTGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAtt                 <  1:850524/76‑1 (MQ=255)
                                                        tGGCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAtttt               <  2:1446980/76‑1 (MQ=255)
                                                         ggCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAttttt              >  2:1689750/1‑76 (MQ=255)
                                                         ggCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAttttt              <  2:126010/76‑1 (MQ=255)
                                                         ggCCAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAttttt              <  2:468384/76‑1 (MQ=255)
                                                           ccAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTa            <  1:265464/76‑1 (MQ=255)
                                                            cAGTTTTCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTAc           >  1:791498/1‑76 (MQ=255)
                                                                tttCCAGGTGCATGCCCAGAGACAGTCCACGGGAACCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAg       <  2:1742770/76‑1 (MQ=255)
                                                                 ttCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAgg      >  2:2178504/1‑76 (MQ=255)
                                                                 ttCCAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAgg      >  2:2117461/1‑76 (MQ=255)
                                                                  tCCAGGTGCATGCCCAGAGACNGTCCCCGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGt     <  2:350480/76‑1 (MQ=255)
                                                                   ccAGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGtt    <  1:518757/76‑1 (MQ=255)
                                                                     aGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg  <  2:390807/76‑1 (MQ=255)
                                                                     aGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg  >  1:1901033/1‑76 (MQ=255)
                                                                     aGGTGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg  <  2:1893129/76‑1 (MQ=255)
                                                                        |                                                                        
CCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAG  >  REL606/3367913‑3368057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A