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
A3 F50 I3 R1 283 58.3 1819865 98.8% 1798026 150.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,182,890 A→G D549G (GAC→GGC)  rpoB → RNA polymerase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,182,8900AG98.0% 168.9 / ‑3.9 51D549G (GAC→GGC) rpoBRNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (19/31);  total (19/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGACGGTG  >  NC_000913/4182748‑4183036
                                                                                                                                              |                                                                                                                                                  
gTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACAcc                                                                                                                                            <  1:741464/151‑1 (MQ=255)
   aaaGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCg                                                                                                                                          >  2:590228/1‑150 (MQ=255)
    aaGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGAc                                                                                                                                        <  1:872790/151‑1 (MQ=255)
     agagTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACt                                                                                                                                       >  2:642199/1‑151 (MQ=255)
              cGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACgg                                                                                                                               <  1:126344/150‑1 (MQ=255)
              cGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACgg                                                                                                                               <  2:404664/150‑1 (MQ=255)
              cGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGt                                                                                                                              >  1:140235/1‑151 (MQ=255)
               ggTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTc                                                                                                                             >  1:26636/1‑151 (MQ=255)
                gTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTcg                                                                                                                            <  2:835284/151‑1 (MQ=255)
                  tCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTcgc                                                                                                                           <  2:12709/150‑1 (MQ=255)
                      gccagcTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATg                                                                                                                      <  2:861800/151‑1 (MQ=255)
                        cagcTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTc                                                                                                                    <  1:20828/151‑1 (MQ=255)
                               ctcAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTcgc                                                                                                                           >  2:347547/1‑137 (MQ=255)
                               ctcAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTcgc                                                                                                                           <  1:347573/137‑1 (MQ=255)
                                 cAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCg                                                                                                              <  1:185052/148‑1 (MQ=255)
                                 cAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaa                                                                                                            <  1:166144/150‑1 (MQ=255)
                                          gACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTTACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGa                                                                                                    >  1:157959/1‑149 (MQ=255)
                                             cAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTc                                                                                               <  2:684119/151‑1 (MQ=255)
                                                aacaacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCg                                                                                             >  1:254480/1‑150 (MQ=255)
                                                    acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACAt                                                                                        <  1:153553/151‑1 (MQ=255)
                                                     cccGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATc                                                                                       <  2:425147/151‑1 (MQ=255)
                                                         cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGt                                                                                    <  2:170266/150‑1 (MQ=255)
                                                              tGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATc                                                                              >  1:778262/1‑151 (MQ=255)
                                                                agaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCa                                                                             >  1:282005/1‑150 (MQ=255)
                                                                 gaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCAAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCaa                                                                            <  2:254710/150‑1 (MQ=255)
                                                                     aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActctc                                                                       <  1:56614/151‑1 (MQ=255)
                                                                         acaAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTc                                                                   >  2:574311/1‑151 (MQ=255)
                                                                          caAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTcc                                                                  <  1:484651/151‑1 (MQ=255)
                                                                                tcgtATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTa                                                             <  1:711263/150‑1 (MQ=255)
                                                                                  gtATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGc                                                          >  1:300670/1‑151 (MQ=255)
                                                                                   tATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGc                                                          >  1:838191/1‑150 (MQ=255)
                                                                                      ctcCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGcac                                                        >  1:637076/1‑149 (MQ=255)
                                                                                          gCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTa                                                  <  1:393666/151‑1 (MQ=255)
                                                                                           cACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTa                                                  >  2:408019/1‑150 (MQ=255)
                                                                                            aCTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAAc                                                >  2:469971/1‑151 (MQ=255)
                                                                                             cTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActct                                                                        <  2:575440/126‑1 (MQ=255)
                                                                                             cTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActct                                                                        >  1:575490/1‑126 (MQ=255)
                                                                                               cGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACg                                               <  1:161254/149‑1 (MQ=255)
                                                                                                ggCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                            <  1:404122/151‑1 (MQ=255)
                                                                                                ggCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                            <  1:678696/151‑1 (MQ=255)
                                                                                                 gCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATa                                           <  1:845920/151‑1 (MQ=255)
                                                                                                 gCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATa                                           <  1:475214/151‑1 (MQ=255)
                                                                                                  cccAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATAc                                          <  2:140212/151‑1 (MQ=255)
                                                                                                    cAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACgg                                        >  1:63728/1‑151 (MQ=255)
                                                                                                        cGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTc                                    >  2:767161/1‑151 (MQ=255)
                                                                                                         ggTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTcc                                   >  2:498573/1‑151 (MQ=255)
                                                                                                              gACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCtt                                 <  2:34583/148‑1 (MQ=255)
                                                                                                              gACCCGTGAACGTGCAGGCTTCGAAGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCtt                                 <  2:315683/148‑1 (MQ=255)
                                                                                                                          tGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATc                    <  1:270796/149‑1 (MQ=255)
                                                                                                                                     aaGTTCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGa       <  1:461259/151‑1 (MQ=255)
                                                                                                                                         tCGAGGCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGACgg    <  2:482255/150‑1 (MQ=255)
                                                                                                                                           gaggCGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGACGgtg  <  1:22677/150‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                  
GTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGACGGTG  >  NC_000913/4182748‑4183036

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A