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
A124 F1 I1 R1 18 228.8 14151462 95.4% 13500494 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 4,164,822 T→C F1323L (TTC→CTC)  rpoB → DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6064,164,8220TC98.7% 959.4 / 1.1 224F1323L (TTC→CTC) rpoBDNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base C (87/134);  total (89/135)
Fisher's exact test for biased strand distribution p-value = 5.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.08e-01

Only 100 of 225 total aligned reads displayed.

GAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTCAA  >  REL606/4164749‑4164895
                                                                         |                                                                         
gAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTc                                                                         >  2:5383286/1‑76 (MQ=255)
 aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCa                                                                        <  2:6769229/76‑1 (MQ=255)
 aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCa                                                                        <  2:6653500/76‑1 (MQ=255)
 aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCa                                                                        >  2:2072855/1‑76 (MQ=255)
 aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCa                                                                        <  2:1771746/76‑1 (MQ=255)
  aCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCaa                                                                       <  2:2260633/76‑1 (MQ=255)
     gTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGt                                                                    <  1:3081867/76‑1 (MQ=255)
      tCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTa                                                                   <  2:6963760/76‑1 (MQ=255)
       cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAt                                                                  >  2:4746119/1‑76 (MQ=255)
       cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAt                                                                  >  1:3799041/1‑76 (MQ=255)
       cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAt                                                                  <  1:3016223/76‑1 (MQ=255)
       cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAt                                                                  >  1:6170362/1‑76 (MQ=255)
        gTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAtt                                                                 <  1:4171147/76‑1 (MQ=255)
        gTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAtt                                                                 >  2:442460/1‑76 (MQ=255)
         tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttg                                                                >  2:3166693/1‑76 (MQ=255)
         tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttg                                                                <  2:3763236/76‑1 (MQ=255)
          aCCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgt                                                               >  2:6214419/1‑76 (MQ=255)
          aCCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgt                                                               <  2:3292293/76‑1 (MQ=255)
          aCCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgt                                                               <  2:4836814/76‑1 (MQ=255)
          aCCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgt                                                               >  1:2774573/1‑76 (MQ=255)
           ccAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgtt                                                              <  2:4465241/76‑1 (MQ=255)
           ccAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgtt                                                              >  1:5935965/1‑76 (MQ=255)
           ccAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgtt                                                              >  2:5812204/1‑76 (MQ=255)
            cAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgttg                                                             <  1:4476479/76‑1 (MQ=255)
            cAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTAttgttg                                                             >  2:3263262/1‑76 (MQ=255)
             aaGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGa                                                            <  2:4969920/76‑1 (MQ=255)
              aGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGaa                                                           <  1:5694963/76‑1 (MQ=255)
               gATGTATAAAAGCATCGTGGACGTCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGaaa                                                          <  2:3916517/76‑1 (MQ=255)
               gATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGaaa                                                          <  2:2334665/76‑1 (MQ=255)
                aTGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAag                                                         <  2:1593356/76‑1 (MQ=255)
                aTGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAag                                                         >  2:6453777/1‑76 (MQ=255)
                  gTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAagag                                                       <  1:2582299/76‑1 (MQ=255)
                   tataAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAgaga                                                      <  1:2230938/76‑1 (MQ=255)
                    ataAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAt                                                     >  1:1076178/1‑76 (MQ=255)
                      aaaaaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAttc                                                   <  2:5873970/76‑1 (MQ=255)
                      aaaaaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttc                                                   <  1:3989820/76‑1 (MQ=255)
                      aaaaaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttc                                                   >  2:6878397/1‑76 (MQ=255)
                      aaaaaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttc                                                   >  1:6592956/1‑76 (MQ=255)
                       aaaaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcg                                                  >  2:4204189/1‑76 (MQ=255)
                         aaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcgtt                                                >  1:164630/1‑76 (MQ=255)
                         aaCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcgtt                                                <  1:3409965/76‑1 (MQ=255)
                          aCATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcgttc                                               >  1:44949/1‑76 (MQ=255)
                           cATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcgttcg                                              >  1:911658/1‑76 (MQ=255)
                           cATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGAttcgttcg                                              <  2:3222899/76‑1 (MQ=255)
                             tCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCt                                            <  1:1899224/76‑1 (MQ=255)
                                tGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTggg                                         >  1:6705543/1‑76 (MQ=255)
                                tGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTggg                                         <  1:6799431/76‑1 (MQ=255)
                                tGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTggg                                         >  2:3506427/1‑76 (MQ=255)
                                 ggACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGt                                        <  2:2222005/76‑1 (MQ=255)
                                 ggACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGt                                        <  1:328093/76‑1 (MQ=255)
                                 ggACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGt                                        <  1:4609847/76‑1 (MQ=255)
                                  gACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTa                                       >  1:3270275/1‑76 (MQ=255)
                                   aCGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTAt                                      <  1:5816071/76‑1 (MQ=255)
                                     ggCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCa                                    <  1:3837103/76‑1 (MQ=255)
                                      gCAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCaa                                   <  1:4811491/76‑1 (MQ=255)
                                       cAACCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAAc                                  >  1:1701710/1‑76 (MQ=255)
                                        aaCCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa                                 >  2:338390/1‑76 (MQ=255)
                                        aaCCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa                                 >  2:240358/1‑76 (MQ=255)
                                        aaCCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa                                 >  1:4876558/1‑76 (MQ=255)
                                        aaCCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa                                 >  1:4546560/1‑76 (MQ=255)
                                         aCCATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACAt                                <  1:6930593/76‑1 (MQ=255)
                                           cATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCg                              >  2:121942/1‑76 (MQ=255)
                                           cATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCg                              >  2:3441726/1‑76 (MQ=255)
                                           cATCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCg                              >  1:6253297/1‑76 (MQ=255)
                                            aTCAGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGa                             >  1:81244/1‑76 (MQ=255)
                                               aGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGaaaa                          >  1:1831302/1‑74 (MQ=255)
                                               aGATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACt                          <  1:6471467/76‑1 (MQ=255)
                                                gATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTg                         >  1:6735142/1‑76 (MQ=255)
                                                gATGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTg                         <  2:6363539/76‑1 (MQ=255)
                                                 aTGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTgg                        <  2:5904238/76‑1 (MQ=255)
                                                 aTGGAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTgg                        <  1:6551353/76‑1 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      <  2:87861/76‑1 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      <  2:5090107/76‑1 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      <  2:5256337/76‑1 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      <  2:3016694/76‑1 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      >  1:7064567/1‑76 (MQ=255)
                                                   ggAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGaa                      <  1:4215510/76‑1 (MQ=255)
                                                    gAGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAg                     <  2:2173775/76‑1 (MQ=255)
                                                     aGCCGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGa                    >  2:4960188/1‑76 (MQ=255)
                                                       ccGGGCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACg                  >  2:2294452/1‑76 (MQ=255)
                                                          ggCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGt               <  2:1523272/76‑1 (MQ=255)
                                                           gCATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTa              <  2:5326222/76‑1 (MQ=255)
                                                            cATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTaa             <  1:6307781/76‑1 (MQ=255)
                                                            cATGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTaa             <  2:6015692/76‑1 (MQ=255)
                                                             aTGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAAt            >  1:1164019/1‑76 (MQ=255)
                                                              tGCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAAtt           <  1:5363944/76‑1 (MQ=255)
                                                               gCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATtc          <  1:4755088/76‑1 (MQ=255)
                                                               gCCAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATtc          <  2:1425891/76‑1 (MQ=255)
                                                                ccAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATtct         <  2:4047408/76‑1 (MQ=255)
                                                                 cAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATtctc        <  1:857747/76‑1 (MQ=255)
                                                                 cAGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATtctc        >  2:4930252/1‑76 (MQ=255)
                                                                  aGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCg       <  1:619207/76‑1 (MQ=255)
                                                                  aGAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCg       >  1:4377300/1‑76 (MQ=255)
                                                                   gAATCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGc      <  1:6912798/76‑1 (MQ=255)
                                                                    aaTCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCt     >  2:2567636/1‑76 (MQ=255)
                                                                    aaTCCCTCAACGTATTGTTGAAAGAGATTCGATCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCt     >  2:5474528/1‑76 (MQ=255)
                                                                     aTCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTc    >  2:2771506/1‑76 (MQ=255)
                                                                     aTCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTc    <  2:3645004/76‑1 (MQ=255)
                                                                     aTCCCTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTc    <  1:2497872/76‑1 (MQ=255)
                                                                       ccTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTCaa  >  2:3046020/1‑76 (MQ=255)
                                                                         |                                                                         
GAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAATTCTCGCTCAA  >  REL606/4164749‑4164895

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A