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
A11 F212 I1 R1 174 80.0 3892211 96.7% 3763768 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,188,787 A→T E1146D (GAA→GAT)  rpoC → RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,188,7870AT84.3% 181.3 / 25.4 71E1146D (GAA→GAT) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base A (5/6);  new base T (27/32);  total (33/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCG  >  NC_000913/4188691‑4188886
                                                                                                |                                                                                                   
gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCa                                                                                                  <  1:1637533/100‑1 (MQ=255)
gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCa                                                                                                  <  1:1637456/100‑1 (MQ=255)
gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCa                                                                                                  <  2:256383/100‑1 (MQ=255)
gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCa                                                                                                  >  1:1222294/1‑100 (MQ=255)
  tCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGCCCTGTTCGATGCAcg                                                                                                <  1:361738/100‑1 (MQ=255)
  tCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCAcg                                                                                                >  2:1744258/1‑100 (MQ=255)
   cAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgt                                                                                               >  2:157573/1‑100 (MQ=255)
   cAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAAACCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgt                                                                                               >  1:1042064/1‑100 (MQ=255)
    aGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgtc                                                                                              >  2:427175/1‑100 (MQ=255)
     gCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgtcg                                                                                             <  2:303545/100‑1 (MQ=255)
       tctGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACgtcgtc                                                                                           <  2:894913/100‑1 (MQ=255)
        ctGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTcc                                                                                          <  1:53122/100‑1 (MQ=255)
         tGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCg                                                                                         >  1:111027/1‑100 (MQ=255)
          ggTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCg                                                                                         >  2:1656546/1‑99 (MQ=255)
           gTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCTTTGCGGACCTGTTCGATTCACGTCGTCCgca                                                                                       <  2:1309683/100‑3 (MQ=255)
             gACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAag                                                                                     >  1:964614/1‑100 (MQ=255)
               cacCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAagag                                                                                   >  2:1525968/1‑100 (MQ=255)
                 cccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGcc                                                                                 <  2:1089682/100‑1 (MQ=255)
                 cccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGcc                                                                                 <  1:743564/100‑1 (MQ=255)
                  ccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCg                                                                                >  2:713950/1‑100 (MQ=255)
                     ggCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCa                                                                             <  2:1861189/100‑1 (MQ=255)
                      gcgcGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCaa                                                                            >  2:166672/1‑100 (MQ=255)
                       cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           >  1:1702357/1‑100 (MQ=255)
                       cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           <  1:156780/100‑1 (MQ=255)
                       cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGACGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           >  2:733483/1‑100 (MQ=255)
                         cgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATcc                                                                         <  2:1825958/100‑1 (MQ=255)
                            aTTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTgg                                                                      <  2:1042065/100‑1 (MQ=255)
                             ttCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGc                                                                     >  2:254452/1‑100 (MQ=255)
                              tCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCt                                                                    <  2:955902/100‑1 (MQ=255)
                              tCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCt                                                                    >  2:415552/1‑100 (MQ=255)
                               ccGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   >  2:298440/1‑100 (MQ=255)
                               ccGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   >  2:96932/1‑100 (MQ=255)
                                cGCAGTAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCGGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGa                                                                  <  2:882853/100‑1 (MQ=255)
                                  cAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGaaa                                                                >  1:127327/1‑100 (MQ=255)
                                  cAGGAAGCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   <  1:340284/97‑1 (MQ=255)
                                  cAGGAACCCGGCGGTACCAAGGACCTCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGaa                                                                 <  1:599497/99‑1 (MQ=255)
                                      aaTCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAg                                                            >  2:181161/1‑100 (MQ=255)
                                       aTCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCGCGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGc                                                           >  1:574724/1‑100 (MQ=255)
                                          cggcggTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGt                                                        <  2:722745/100‑1 (MQ=255)
                                              ggTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCg                                                    <  1:427173/100‑1 (MQ=255)
                                                  ccAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTc                                                <  1:275503/100‑1 (MQ=255)
                                                   cAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTcc                                               <  2:1694034/100‑1 (MQ=255)
                                                      ggACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTc                                            <  2:667791/100‑1 (MQ=255)
                                                      ggACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTc                                            <  1:233763/100‑1 (MQ=255)
                                                        aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  2:381113/100‑1 (MQ=255)
                                                        aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  1:1577541/100‑1 (MQ=255)
                                                        aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  2:475690/100‑1 (MQ=255)
                                                         cATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGt                                         >  2:1503627/1‑100 (MQ=255)
                                                         cATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGt                                         <  1:1722000/100‑1 (MQ=255)
                                                          aTCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTa                                        <  2:944791/100‑1 (MQ=255)
                                                            cACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTaaa                                      <  1:1866163/100‑1 (MQ=255)
                                                             cgatctggtCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTaaan                                     <  1:107051/95‑2 (MQ=255)
                                                             aCCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAg                                     <  1:1744247/100‑1 (MQ=255)
                                                              ccGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGa                                    >  1:1638222/1‑100 (MQ=255)
                                                               cGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGan                                   <  1:1656536/100‑2 (MQ=255)
                                                                 gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCCGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 >  2:961604/1‑100 (MQ=255)
                                                                 gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 <  2:321119/100‑1 (MQ=255)
                                                                 gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 >  2:424529/1‑100 (MQ=255)
                                                                   ngtCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGagatcg                               >  2:107051/2‑95 (MQ=255)
                                                                    gtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCaa                              >  1:1681083/1‑100 (MQ=255)
                                                                        gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAgg                           <  1:331397/99‑1 (MQ=255)
                                                                        gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  1:628652/1‑100 (MQ=255)
                                                                        gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  1:17245/1‑100 (MQ=255)
                                                                        gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  2:394113/1‑100 (MQ=255)
                                                                         ccGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTa                         >  2:1292209/1‑100 (MQ=255)
                                                                          cgcgcgTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTaa                        >  1:434592/1‑100 (MQ=255)
                                                                                  gCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACgtcgtc                <  1:713949/100‑1 (MQ=255)
                                                                                       ccTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGtt           <  1:756328/100‑1 (MQ=255)
                                                                                       ccTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGtt           >  2:535940/1‑100 (MQ=255)
                                                                                          gTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATc        <  1:691751/100‑1 (MQ=255)
                                                                                              gAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCAccc    >  1:1716279/1‑100 (MQ=255)
                                                                                                aGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCg  <  1:1764884/100‑1 (MQ=255)
                                                                                                |                                                                                                   
GATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCG  >  NC_000913/4188691‑4188886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A