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 F28 I1 R1 132 43.0 1464274 99.1% 1451095 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,029,739 (A)8→9 coding (231/1191 nt) rlmI ← 23S rRNA m(5)C1962 methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,029,7311.A97.8% 149.7 / ‑3.7 46coding (239/1191 nt)rlmI23S rRNA m(5)C1962 methyltransferase
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base A (19/26);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 4.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

GCACCAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑AAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAGG  >  NC_000913/1029594‑1029865
                                                                                                                                           |                                                                                                                                      
gcaCCAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑aa                                                                                                                                      >  1:131939/1‑140 (MQ=255)
gcaCCAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑aa                                                                                                                                      >  1:171802/1‑140 (MQ=255)
gcaCCAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑aa                                                                                                                                      >  2:224794/1‑140 (MQ=255)
   ccAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑aaaaa                                                                                                                                   >  1:435413/1‑140 (MQ=255)
           ttACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑aaaaaaaaagcaa                                                                                                                           <  2:241889/140‑6 (MQ=255)
              ccGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGt                                                                                                                         >  1:31140/1‑140 (MQ=255)
                 aaaCGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGa                                                                                                                      <  1:71109/140‑1 (MQ=255)
                 aaaCGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGa                                                                                                                      >  2:275706/1‑140 (MQ=255)
                     gatcgatAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGa                                                                                                                  >  1:305667/1‑140 (MQ=255)
                      atcgatAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGAc                                                                                                                 >  1:611226/1‑140 (MQ=255)
                         gatAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCa                                                                                                              <  2:378506/140‑1 (MQ=255)
                         gatAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCa                                                                                                              <  2:196980/140‑1 (MQ=255)
                           tAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGa                                                                                                            <  1:100512/140‑1 (MQ=255)
                                aTACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAAAGTCGATAGACTCAGACgggg                                                                                                       >  2:457416/1‑139 (MQ=255)
                                  aCCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCa                                                                                                     >  1:474736/1‑140 (MQ=255)
                                   cccGGCAGGCCATCAGATTCCCCGGAGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCaa                                                                                                    <  1:563544/140‑1 (MQ=255)
                                     cGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTACAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAAc                                                                                                  >  2:232282/1‑140 (MQ=255)
                                      ggCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGCGGGG‑AAAAAAAAAAAAAGTCGGTAGACCCAGACGGGGCAAAca                                                                                                 >  2:401228/1‑139 (MQ=255)
                                        cAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCGTTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCaa                                                                                                    >  2:391638/1‑135 (MQ=255)
                                        cAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCGTTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCaa                                                                                                    <  1:391638/135‑1 (MQ=255)
                                        cAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTc                                                                                               >  2:55655/1‑140 (MQ=255)
                                                     tctcCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAAAGTCCAGACGCGCGccc                                                                                  >  2:230330/1‑140 (MQ=255)
                                                          ggCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGAtt                                                                             <  1:55655/140‑1 (MQ=255)
                                                          ggCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGAtt                                                                             >  2:190777/1‑140 (MQ=255)
                                                             gATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGc                                                                          >  1:205433/1‑140 (MQ=255)
                                                              aTTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCg                                                                         <  2:77547/140‑1 (MQ=255)
                                                                        aGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGa                                                               >  2:390965/1‑140 (MQ=255)
                                                                            gTCGAGGCCATCTTTTTGCACCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATaa                                                           >  1:678370/1‑140 (MQ=255)
                                                                                       cTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑AAAAAAAAGCAATGTCGATAGACTCAGACGGGGCCAACGGCCAGACGCGCGCCCGGATTTTCGAAGCTGGCGAATAAACGCCGCGTGCt                                               >  2:618812/1‑140 (MQ=255)
                                                                                         ttttGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTa                                              <  2:131939/140‑1 (MQ=255)
                                                                                         ttttGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTa                                              <  2:611226/140‑1 (MQ=255)
                                                                                          tttGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTaa                                             >  2:498137/1‑140 (MQ=255)
                                                                                               gccagccaGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCAtt                                        <  1:275706/140‑1 (MQ=255)
                                                                                                   gccagTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTcc                                    >  2:550460/1‑140 (MQ=255)
                                                                                                    ccagTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTccc                                   <  1:401228/140‑1 (MQ=255)
                                                                                                       gTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtga                                <  1:478756/140‑1 (MQ=255)
                                                                                                       gTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtga                                <  2:435413/140‑1 (MQ=255)
                                                                                                         cACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtgatg                              <  1:180580/140‑1 (MQ=255)
                                                                                                         cACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtgatg                              <  1:232282/140‑1 (MQ=255)
                                                                                                         cACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtgatg                              <  2:31140/140‑1 (MQ=255)
                                                                                                         cACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCtgatg                              <  1:390965/140‑1 (MQ=255)
                                                                                                           cGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTgatgat                            >  2:692554/1‑140 (MQ=255)
                                                                                                           cGCCATTTTTGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTgatgat                            <  2:171802/140‑1 (MQ=255)
                                                                                                                  tttGTGCTTGTTGCAAACGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAat                     >  2:563241/1‑140 (MQ=255)
                                                                                                                                aaaCGGC‑GGGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCAc       <  2:205433/140‑1 (MQ=255)
                                                                                                                                    ggc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAg   >  1:207489/1‑140 (MQ=255)
                                                                                                                                    ggc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAg   <  1:498137/140‑1 (MQ=255)
                                                                                                                                     gc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAgg  <  1:283371/140‑1 (MQ=255)
                                                                                                                                     gc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAgg  <  1:550460/140‑1 (MQ=255)
                                                                                                                                     gc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAgg  <  1:190777/140‑1 (MQ=255)
                                                                                                                                     gc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAgg  <  1:563241/140‑1 (MQ=255)
                                                                                                                                     gc‑ggGAAAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAgg  <  2:678370/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                      
GCACCAGAAAATTACCGAAACGATCGATAGTAATACCCGGCAGGCCATCAGATTCTCCGGCGATTAAACGATAGCTGTCGAGGCCATCTTTTTGCGCCAGCCAGTCACGCCATTTTTGTGCTTGTTGCAAACGGC‑GGG‑AAAAAAAAGCAATGTCGATAGACTCAGACGGGTCAAACGTCCAGACGCGCGCCCGGATTTGCGAAGCTGGCGAATAAGCGCCGCGTGCTAACCATTTTCCCTGATGATCAACAATATCGATGGTTTCACCGAGG  >  NC_000913/1029594‑1029865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A