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
A89 F1 I1 R1 15 55.0 3646496 95.5% 3482403 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 4,163,089 A→C E745A (GAA→GCA)  rpoB → DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6064,163,0890AC97.2% 295.6 / ‑2.4 72E745A (GAA→GCA) rpoBDNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base C (34/36);  total (35/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGCC  >  REL606/4163016‑4163161
                                                                         |                                                                        
ggtggtgTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAg                                                                        >  1:1108152/1‑76 (MQ=255)
 gtggtgTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGc                                                                       <  2:1220764/76‑1 (MQ=255)
   ggtgTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGcagcag                                                                     >  1:1278209/1‑76 (MQ=255)
       tCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTAt                                                                 <  1:1424474/76‑1 (MQ=255)
       tCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTAt                                                                 <  2:1553319/76‑1 (MQ=255)
         gTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCg                                                               <  2:1800490/76‑1 (MQ=255)
         gTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCg                                                               <  2:1354081/76‑1 (MQ=255)
         gTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCg                                                               <  1:375004/76‑1 (MQ=255)
         gTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGAGCAGCAGGTATCg                                                               >  1:1746786/1‑76 (MQ=255)
          ttCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGa                                                              >  2:1220189/1‑76 (MQ=255)
          ttCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGa                                                              >  1:1129546/1‑76 (MQ=255)
           tCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGAc                                                             >  2:1635974/1‑76 (MQ=255)
            cAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGGGCAGCAGGTATCGACa                                                            >  1:428472/1‑76 (MQ=255)
              gTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATc                                                          <  1:669146/76‑1 (MQ=255)
               tACGTGGATCCTTCCCGTATCGTTAGCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATcc                                                         <  1:1249731/76‑2 (MQ=255)
                aCGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTa                                                        <  1:1155965/76‑1 (MQ=255)
                aCGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTa                                                        >  1:319435/1‑76 (MQ=255)
                  gTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACa                                                      <  2:857091/76‑1 (MQ=255)
                  gTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACa                                                      >  1:1477348/1‑76 (MQ=255)
                   tGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACaa                                                     <  2:853144/76‑1 (MQ=255)
                    ggATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAAc                                                    >  2:389047/1‑76 (MQ=255)
                       tGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTg                                                 <  1:1334299/76‑1 (MQ=255)
                       tGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTg                                                 <  1:1103443/76‑1 (MQ=255)
                       tGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTg                                                 <  1:632194/76‑1 (MQ=255)
                       tGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGAATCCGGGTGCAGCAGGAATCGACATCTACAACCTg                                                 <  2:751985/76‑1 (MQ=255)
                        gCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGa                                                >  1:821107/1‑76 (MQ=255)
                          ttCCCGTATCGTTATCAAATTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGAcc                                              <  1:392566/76‑1 (MQ=255)
                           tCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCa                                             >  1:1517548/1‑76 (MQ=255)
                              cGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAAt                                          >  1:1718105/1‑76 (MQ=255)
                               gTATCGTTATCAAATTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATa                                         <  1:392776/76‑1 (MQ=255)
                               gTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACAAAATa                                         <  2:868970/76‑1 (MQ=255)
                                tATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATac                                        >  2:667826/1‑76 (MQ=255)
                                 aTCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATaca                                       >  1:1682998/1‑76 (MQ=255)
                                      tATCAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGCATCGACATCTACAACCCGACCAAATACAcccct                                  >  2:310274/1‑74 (MQ=255)
                                         cAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCt                               >  1:1805366/1‑76 (MQ=255)
                                         cAAAGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCt                               >  1:439170/1‑76 (MQ=255)
                                          aaaGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACTCCCGTTCTa                              <  1:1325343/76‑1 (MQ=255)
                                          aaaGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCtt                              <  1:1005811/76‑2 (MQ=255)
                                          aaaGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTa                              <  2:1441304/76‑1 (MQ=255)
                                          aaaGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTa                              >  2:564826/1‑76 (MQ=255)
                                            aGTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAAc                            >  1:1767606/1‑76 (MQ=255)
                                            aGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAAc                            >  2:1776619/1‑76 (MQ=255)
                                             gTTAACGAATGCGAGAGGTATCCGTGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACGCCCGTTCTAAcc                           <  2:1260339/76‑1 (MQ=255)
                                             gTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAAcc                           <  2:1374332/76‑1 (MQ=255)
                                             gTTAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAAcc                           <  1:1617036/76‑1 (MQ=255)
                                              ttAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCa                          >  1:1001387/1‑76 (MQ=255)
                                              ttAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACAAAATACACCCGTCCTAACCa                          >  1:758385/1‑76 (MQ=255)
                                               tAACGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAg                         >  1:1243929/1‑76 (MQ=255)
                                                aaCGAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGa                        >  1:1444928/1‑76 (MQ=255)
                                                  cGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAac                      <  1:298340/76‑1 (MQ=255)
                                                   gAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAaca                     >  1:1757225/1‑76 (MQ=255)
                                                   gAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAaca                     <  1:1756411/76‑1 (MQ=255)
                                                   gAAGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAaca                     >  1:1206102/1‑76 (MQ=255)
                                                     aGACGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACAcc                   <  1:1170897/76‑1 (MQ=255)
                                                       aCGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTg                 <  1:980147/76‑1 (MQ=255)
                                                       aCGAGATGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTg                 >  1:275769/1‑76 (MQ=255)
                                                           gaTGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATc             <  2:1729839/76‑1 (MQ=255)
                                                            aTGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCa            >  2:97806/1‑76 (MQ=255)
                                                            aTGTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCa            <  1:624662/76‑1 (MQ=255)
                                                              gTATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAAc          >  1:413063/1‑76 (MQ=255)
                                                               tATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACCCCCGTTCTAACCAGAACACCTGTATCaaac         <  1:830734/76‑3 (MQ=255)
                                                               tATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAAcc         >  2:1670030/1‑76 (MQ=255)
                                                               tATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAAcc         <  1:750558/76‑1 (MQ=255)
                                                               tATCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAAcc         >  1:1387126/1‑76 (MQ=255)
                                                                aTCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCa        >  2:1479773/1‑76 (MQ=255)
                                                                aTCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCa        >  1:821371/1‑76 (MQ=255)
                                                                aTCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCa        <  2:567120/76‑1 (MQ=255)
                                                                aTCCGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCa        <  1:1198877/76‑1 (MQ=255)
                                                                   cGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGAt     >  2:263330/1‑76 (MQ=255)
                                                                   cGGGTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGAt     <  2:80369/76‑1 (MQ=255)
                                                                    gggTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATg    <  2:1032742/76‑1 (MQ=255)
                                                                    gggTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATg    <  1:1294723/76‑1 (MQ=255)
                                                                     ggTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGc   >  2:1496725/1‑76 (MQ=255)
                                                                      gTGCAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGcc  <  2:570070/76‑1 (MQ=255)
                                                                         |                                                                        
GGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGCC  >  REL606/4163016‑4163161

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A