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 F142 I0 R1 175 91.2 4812830 94.5% 4548124 99.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,728,444 C→A 100% T33N (ACC→AAC)  rnt → RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,728,4440CA98.5% 216.7 / ‑3.6 68T33N (ACC→AAC) rntRNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (40/27);  total (41/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01

TGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCA  >  NC_000913/1728348‑1728538
                                                                                                |                                                                                              
tGTCCGATAACGCTCAACTTACCGGTCTGTGCGTCCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGa                                                                                             <  2:1327214/100‑1 (MQ=255)
tGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGa                                                                                             <  1:1272096/100‑1 (MQ=255)
  tCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATg                                                                                           <  2:954605/100‑1 (MQ=255)
    cGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgcg                                                                                         >  1:1773851/1‑100 (MQ=255)
    cGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgcg                                                                                         >  2:316765/1‑100 (MQ=255)
          cGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCtt                                                                                   >  2:1341828/1‑100 (MQ=255)
            cTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTga                                                                                 <  1:709356/100‑1 (MQ=255)
             tCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgag                                                                                <  1:60498/100‑1 (MQ=255)
              cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgaga                                                                               <  1:1419933/100‑1 (MQ=255)
              cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgaga                                                                               >  2:2128452/1‑100 (MQ=255)
              cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTga                                                                                 <  2:68810/98‑1 (MQ=255)
               aaCTTAGCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCATGTTGTGATCGATGTTGAAACAGCCGGATTTTACGCCAAAAACGATGCGCTGCTTgag                                                                                <  2:110778/98‑1 (MQ=255)
               aaCTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGAt                                                                              >  2:158213/1‑100 (MQ=255)
                aCTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGAtt                                                                             >  1:585193/1‑100 (MQ=255)
                  ttACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACCGCCGGATTTAACTCCAAAAACGATGCGCTGCTTGAGATTgc                                                                           >  2:988438/1‑100 (MQ=255)
                   tACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgcc                                                                          >  2:521795/1‑100 (MQ=255)
                   tACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgcc                                                                          >  1:1175487/1‑100 (MQ=255)
                    aCCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgccg                                                                         <  2:1609645/100‑1 (MQ=255)
                     ccGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgccgc                                                                        >  1:1756571/1‑100 (MQ=255)
                         tCTGTGCGATCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATc                                                                    <  2:1644411/100‑1 (MQ=255)
                          cTGTGCGACCGTTTTCGTGATTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATc                                                                    >  2:2244272/1‑99 (MQ=255)
                           tgtgCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAc                                                                  >  1:1227588/1‑100 (MQ=255)
                             tgCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAccc                                                                >  2:358092/1‑100 (MQ=255)
                                   cGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaaaa                                                          >  2:1061011/1‑100 (MQ=255)
                                    gTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAAt                                                         >  1:1321411/1‑100 (MQ=255)
                                     ttttCGTGGTTTGTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAATAACGATGCGCTGCTTGAGATTGCCGCCATTACCCTGAAAATg                                                        <  2:46315/100‑1 (MQ=255)
                                       ttCGTGGTTTTTATCCTGTTGTGATCGATGTTAAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGa                                                      >  1:2279985/1‑100 (MQ=255)
                                        tCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGAt                                                     <  2:110960/100‑1 (MQ=255)
                                        tCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGAt                                                     <  2:269465/100‑1 (MQ=255)
                                         cGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATg                                                    <  2:1075429/100‑1 (MQ=255)
                                             gTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACa                                                >  1:32728/1‑100 (MQ=255)
                                              tttttATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACaa                                               >  1:907584/1‑100 (MQ=255)
                                               ttttATACTGTTGTGATCGATGTTGAAACAGCCGGATTTAAGGCAAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAAGGGATGaa                                                  >  2:1515915/1‑96 (MQ=255)
                                                   aTCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctg                                          >  1:2000118/1‑100 (MQ=255)
                                                     ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                        <  1:1742178/100‑1 (MQ=255)
                                                     ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                        >  2:2174049/1‑100 (MQ=255)
                                                      cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGTCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                        <  2:1059624/99‑1 (MQ=255)
                                                      cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                       >  1:2248077/1‑100 (MQ=255)
                                                      cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                       <  1:615080/100‑1 (MQ=255)
                                                          tgtgATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATg                                   <  2:839592/100‑1 (MQ=255)
                                                          tgtgATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATg                                   >  2:1506474/1‑100 (MQ=255)
                                                           gtgATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGc                                  >  1:1444791/1‑100 (MQ=255)
                                                           gtgATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGc                                  >  2:1008886/1‑100 (MQ=255)
                                                            tgATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGcc                                 >  2:1145267/1‑100 (MQ=255)
                                                             gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGcc                                 >  2:393122/1‑99 (MQ=255)
                                                             gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                                >  1:974865/1‑100 (MQ=255)
                                                              aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCgg                               <  1:1355568/100‑1 (MQ=255)
                                                              aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                                >  1:1829172/1‑99 (MQ=255)
                                                              aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                                <  2:2218513/99‑1 (MQ=255)
                                                                 gATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCgg                               <  2:1069615/97‑1 (MQ=255)
                                                                 gATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATGGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGac                             <  1:583659/99‑1 (MQ=255)
                                                                      tGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCATGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACcaca                       >  2:1665636/1‑100 (MQ=255)
                                                                      tGAAACAGCCGGAGTTAACGCTAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACcaca                       >  1:1611103/1‑100 (MQ=255)
                                                                        aaaCAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacatt                     >  1:1339194/1‑100 (MQ=255)
                                                                            aGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattacat                 <  2:1227575/100‑1 (MQ=255)
                                                                             gCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattacat                 >  1:1298702/1‑99 (MQ=255)
                                                                               cGGATTTAACGCTAAAAACGATGCGCTGCTTGAGATTTCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTc              <  2:1611083/100‑1 (MQ=255)
                                                                                    ttAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGt         <  1:2083573/100‑1 (MQ=255)
                                                                                     tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc        >  2:2061776/1‑100 (MQ=255)
                                                                                     tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc        >  2:1779779/1‑100 (MQ=255)
                                                                                     tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc        >  1:575475/1‑100 (MQ=255)
                                                                                      aaCGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCg       <  2:1756550/100‑1 (MQ=255)
                                                                                      aaCGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCg       <  1:1894827/100‑1 (MQ=255)
                                                                                        cGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGaa     >  1:1979608/1‑100 (MQ=255)
                                                                                          ccAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCGACGTCGAAcc   >  2:2357083/1‑100 (MQ=255)
                                                                                          ccAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAAcc   >  2:950109/1‑100 (MQ=255)
                                                                                          ccAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAAcc   >  2:1224060/1‑100 (MQ=255)
                                                                                           cAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCa  >  1:1201330/1‑100 (MQ=255)
                                                                                                |                                                                                              
TGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCA  >  NC_000913/1728348‑1728538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A