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
A101 F1 I1 R1 20 160.9 10398134 92.8% 9649468 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,145,750 C→T intergenic (+81/‑114) dnaG → / → rpoD DNA primase/RNA polymerase sigma factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,145,7500CT98.8% 630.1 / ‑1.9 164intergenic (+81/‑114)dnaG/rpoDDNA primase/RNA polymerase sigma factor
Reads supporting (aligned to +/- strand):  ref base C (0/2);  new base T (92/70);  total (92/72)
Fisher's exact test for biased strand distribution p-value = 1.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.27e-01

Only 100 of 166 total aligned reads displayed.

CTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATC  >  REL606/3145678‑3145822
                                                                        |                                                                        
cTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCt                                                                       >  2:2301175/1‑76 (MQ=255)
cTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCt                                                                       >  1:2313211/1‑76 (MQ=255)
cTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCt                                                                       >  1:1742805/1‑76 (MQ=255)
 ttAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTc                                                                      >  2:1258157/1‑76 (MQ=255)
 ttAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTc                                                                      >  1:2205062/1‑76 (MQ=255)
  tAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCg                                                                     >  2:4080953/1‑76 (MQ=255)
  tAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCg                                                                     >  2:1391440/1‑76 (MQ=255)
   aaGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGt                                                                    >  2:1834209/1‑76 (MQ=255)
   aaGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGt                                                                    >  2:513685/1‑76 (MQ=255)
   aaGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGt                                                                    >  2:238528/1‑76 (MQ=255)
      tGCCGAAGAGCGAGCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAt                                                                 <  1:2259514/76‑1 (MQ=255)
       gCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAtt                                                                >  1:4899160/1‑76 (MQ=255)
       gCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAtt                                                                <  1:4256602/76‑1 (MQ=255)
       gCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAtt                                                                <  2:3629968/76‑1 (MQ=255)
       gCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAtt                                                                <  1:3994282/76‑1 (MQ=255)
       cgcGAAGAGCTATCGGAACCCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAAtt                                                                <  2:2594105/74‑1 (MQ=255)
         cGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTAt                                                              >  2:4646941/1‑76 (MQ=255)
         cGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTAt                                                              >  2:2483012/1‑76 (MQ=255)
         cGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTAt                                                              <  1:3762200/76‑1 (MQ=255)
          gAAGAGCGTCCGGGAGCCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATc                                                             <  2:4785074/76‑1 (MQ=255)
          gAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATc                                                             >  2:35700/1‑76 (MQ=255)
          gAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATc                                                             >  1:2795316/1‑76 (MQ=255)
           aaGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCg                                                            >  2:343650/1‑76 (MQ=255)
           aaGAGCGAGCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCg                                                            <  1:4802143/76‑1 (MQ=255)
            agagCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGt                                                           >  2:1738226/1‑76 (MQ=255)
            agagCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGt                                                           >  2:1025306/1‑76 (MQ=255)
            agagCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGt                                                           >  2:2968793/1‑76 (MQ=255)
              ggCGATGGGAACGCCCCCGCCAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTg                                                         <  2:4662626/75‑1 (MQ=255)
                 gATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCg                                                      <  1:2170252/76‑1 (MQ=255)
                    cGGGAAGCCCCCGACAGCCGCACTGAGCGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCggga                                                   >  1:2827287/1‑74 (MQ=255)
                    cGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTa                                                   >  2:1372674/1‑76 (MQ=255)
                    cGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTa                                                   >  1:4641182/1‑76 (MQ=255)
                    cGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTa                                                   >  2:2610874/1‑76 (MQ=255)
                    cGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTa                                                   >  1:4991847/1‑76 (MQ=255)
                     gggAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTaa                                                  <  2:1116092/76‑1 (MQ=255)
                     gggAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTaa                                                  >  1:549469/1‑76 (MQ=255)
                       gAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAaac                                                <  1:2463998/76‑1 (MQ=255)
                         gccccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAaacaa                                              <  2:4982696/74‑1 (MQ=255)
                          gCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAaacaac                                             <  1:320568/76‑1 (MQ=255)
                          gCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAaacaac                                             >  1:4713595/1‑76 (MQ=255)
                           cccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAAcc                                            >  2:2561592/1‑76 (MQ=255)
                           cccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGCAAACAAcc                                            >  2:4051728/1‑76 (MQ=255)
                            ccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCg                                           <  1:3144125/76‑1 (MQ=255)
                            ccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCg                                           <  1:2074215/76‑1 (MQ=255)
                            ccccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCg                                           <  1:387806/76‑1 (MQ=255)
                              ccGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGtt                                         <  2:2178759/76‑1 (MQ=255)
                                gccAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTgg                                       <  2:3221863/74‑1 (MQ=255)
                                gACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTgg                                       <  1:2636801/76‑1 (MQ=255)
                                 ccAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGa                                      <  1:1667089/75‑1 (MQ=255)
                                 aCAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGa                                      >  2:4106783/1‑76 (MQ=255)
                                 aCAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGa                                      <  2:1937698/76‑1 (MQ=255)
                                    gCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGAttt                                   <  1:844307/76‑1 (MQ=255)
                                    gCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGAttt                                   <  2:2779486/76‑1 (MQ=255)
                                     ccGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTc                                  <  1:1498032/76‑1 (MQ=255)
                                     ccGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTc                                  <  2:3110901/76‑1 (MQ=255)
                                     ccGCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTc                                  <  2:195372/76‑1 (MQ=255)
                                       gCACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAg                                >  1:1867703/1‑76 (MQ=255)
                                        cACTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGc                               >  1:2917361/1‑76 (MQ=255)
                                          cTGAGAGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGt                             >  2:410629/1‑76 (MQ=255)
                                            gagaGGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTa                           <  1:3316581/76‑1 (MQ=255)
                                             agagGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTaa                          >  2:3472079/1‑76 (MQ=255)
                                             agagGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTaa                          >  1:655399/1‑76 (MQ=255)
                                              gagGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAAc                         >  2:3233795/1‑76 (MQ=255)
                                              gagGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAAc                         >  1:65042/1‑76 (MQ=255)
                                               agGCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACg                        >  1:1175514/1‑76 (MQ=255)
                                                ggCAGCGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACgg                       <  2:3190982/76‑1 (MQ=255)
                                                     gggCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGaa                  <  2:2859578/75‑1 (MQ=255)
                                                     cGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTgga                  >  2:4885080/1‑74 (MQ=255)
                                                     cGGCAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGaa                  <  2:4776986/76‑1 (MQ=255)
                                                        cAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGa               >  1:2337037/1‑76 (MQ=255)
                                                        cAAATATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGa               >  2:3864514/1‑76 (MQ=255)
                                                         aaaTATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAgggc              >  1:4991472/1‑74 (MQ=255)
                                                         aaaTATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGAc              >  2:4568831/1‑76 (MQ=255)
                                                         aaaTATATAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGAc              <  2:3651302/76‑1 (MQ=255)
                                                           atatatAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGCTTTCAGCGTTAACGGCTGGAGGAAAt            >  1:4326501/1‑76 (MQ=255)
                                                           atatatAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGc                               >  1:4598066/1‑57 (MQ=255)
                                                           atatatAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGc                               <  2:4598066/57‑1 (MQ=255)
                                                           atatatAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACAt            <  2:208522/76‑1 (MQ=255)
                                                           atatatAAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACAt            >  2:1060921/1‑76 (MQ=255)
                                                            tatataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACaac           >  2:3339900/1‑74 (MQ=255)
                                                             atataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGGCATCg          >  2:1251915/1‑76 (MQ=255)
                                                             atataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCg          >  2:3097319/1‑76 (MQ=255)
                                                             atataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCg          >  1:5120476/1‑76 (MQ=255)
                                                             atataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCg          >  1:3709385/1‑76 (MQ=255)
                                                             atataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCg          >  2:1578699/1‑76 (MQ=255)
                                                              tataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCgg         <  1:238528/76‑1 (MQ=255)
                                                              tataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCgg         <  1:1834209/76‑1 (MQ=255)
                                                               ataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCggg        <  2:2254862/76‑1 (MQ=255)
                                                               ataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCggg        >  1:5122646/1‑76 (MQ=255)
                                                               ataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCggg        <  1:4136115/76‑1 (MQ=255)
                                                               ataAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAAGGCATCggg        >  1:502310/1‑76 (MQ=255)
                                                               agaaGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCggg        <  1:4498824/74‑1 (MQ=255)
                                                                taAGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTACCGGCTGAAGGACATCgggg       >  1:3940270/1‑75 (MQ=255)
                                                                 aaGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCggggc      >  2:175476/1‑74 (MQ=255)
                                                                 aaGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTc      <  2:649599/76‑1 (MQ=255)
                                                                 aaGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTc      <  1:2174733/76‑1 (MQ=255)
                                                                  aGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCa     <  1:4285034/76‑1 (MQ=255)
                                                                  aGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCa     >  1:1358325/1‑76 (MQ=255)
                                                                  aGTACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGAAAACGGGGCa     >  2:3515107/1‑76 (MQ=255)
                                                                    tACGTCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAAt   <  2:2851120/76‑1 (MQ=255)
                                                                        |                                                                        
CTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCACTGAGAGGCAGCGGCAAATATATAAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATC  >  REL606/3145678‑3145822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A