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 161 75.5 2581324 99.3% 2563254 138.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,398,578 (C)5→6 coding (1167/1848 nt) mutL → DNA mismatch repair protein MutL

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,398,5731.C97.7% 150.1 / ‑3.1 44coding (1162/1848 nt)mutLDNA mismatch repair protein MutL
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (25/18);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 4.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01

CGATGAACCCCAACCTGCACCGCGTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTG‑CCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTGCGGCGAA  >  NC_000913/4398434‑4398703
                                                                                                                                            |                                                                                                                                   
cGATGAACCCCAACCTGCACCGCGTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTg                                                                                                                                      <  1:1128464/140‑1 (MQ=255)
                 cACCGCGTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATgc                                                                                                                    >  1:976085/1‑140 (MQ=255)
                 cACCGCGTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATgc                                                                                                                    >  2:565378/1‑140 (MQ=255)
                     gcgTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAg                                                                                                                >  1:275122/1‑140 (MQ=255)
                      cgTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATg                                                                                                                     <  1:142499/134‑1 (MQ=255)
                      cgTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATg                                                                                                                     >  2:142499/1‑134 (MQ=255)
                      cgTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGc                                                                                                               <  2:831504/140‑1 (MQ=255)
                      cgTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGc                                                                                                               >  1:461799/1‑140 (MQ=255)
                          ccATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAgg                                                                                                           <  1:491465/140‑1 (MQ=255)
                                cGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCa                                                                                                     >  2:417277/1‑140 (MQ=255)
                                      aCCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACa                                                                                               <  1:1151055/140‑1 (MQ=255)
                                       ccGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAg                                                                                              >  2:1000792/1‑140 (MQ=255)
                                        cgcgTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGc                                                                                             <  2:58441/140‑1 (MQ=255)
                                         gcgTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCa                                                                                            <  1:1121115/140‑1 (MQ=255)
                                           gTGGCTGCGGGGCGCAATCACTTTGCAGAACCCGCAGCTCCTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTG‑CCCCCTTGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAg                                                                                          <  2:1139382/140‑1 (MQ=255)
                                           gTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAg                                                                                          >  2:816775/1‑140 (MQ=255)
                                               cggcggGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGa                                                                                      <  2:123200/140‑1 (MQ=255)
                                                   ggggCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAgtg                                                                                  <  1:631450/140‑1 (MQ=255)
                                                          aaTCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGcc                                                                           <  2:461799/140‑1 (MQ=255)
                                                                    cAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCa                                                                 <  1:1152576/140‑1 (MQ=255)
                                                                            gCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCcg                                                         >  2:832974/1‑140 (MQ=255)
                                                                                     gAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGc                                                >  1:1063976/1‑140 (MQ=255)
                                                                                      aGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCa                                               >  1:104819/1‑140 (MQ=255)
                                                                                          ggTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCtaaaa                                           >  2:1185899/1‑140 (MQ=255)
                                                                                                     gcTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGcc                                >  2:300518/1‑140 (MQ=255)
                                                                                                       tACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCgg                              <  1:133133/140‑1 (MQ=255)
                                                                                                       tACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCgg                              <  2:1221399/140‑1 (MQ=255)
                                                                                                              cTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCgg                              >  2:950102/1‑133 (MQ=255)
                                                                                                              cTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCgg                              <  1:950102/133‑1 (MQ=255)
                                                                                                              cTGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCa                       <  2:449952/140‑1 (MQ=255)
                                                                                                               tGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAg                      >  1:561359/1‑140 (MQ=255)
                                                                                                               tGCGCCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAg                      >  1:125503/1‑140 (MQ=255)
                                                                                                                 cgcCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGa                    >  1:320352/1‑140 (MQ=255)
                                                                                                                 cgcCAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGa                    >  2:608960/1‑140 (MQ=255)
                                                                                                                   ccAGCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAAc                  >  2:271576/1‑140 (MQ=255)
                                                                                                                      gCATCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTg               >  2:26204/1‑140 (MQ=255)
                                                                                                                        aTCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCa             >  2:169019/1‑140 (MQ=255)
                                                                                                                        aTCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCa             >  1:847756/1‑140 (MQ=255)
                                                                                                                         tCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCAc            <  1:768014/140‑1 (MQ=255)
                                                                                                                         tCAGGCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCAc            <  2:320352/140‑1 (MQ=255)
                                                                                                                            ggCAGTCGTCCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTg         >  2:164867/1‑140 (MQ=255)
                                                                                                                                 tcgtcCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTgcggcg    >  1:108622/1‑140 (MQ=255)
                                                                                                                                 tcgtcCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTgcggcg    >  1:923075/1‑140 (MQ=255)
                                                                                                                                  cgtcCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTGCGGCGa   <  1:816775/140‑1 (MQ=255)
                                                                                                                                  cgtcCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTGCGGCGa   >  1:1161288/1‑140 (MQ=255)
                                                                                                                                   gtcCGGCTGCCCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTGCGGCGaa  <  1:271576/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                   
CGATGAACCCCAACCTGCACCGCGTTCCATTCCGGAAAACCGCGTGGCGGCGGGGCGCAATCACTTTGCAGAACCGGCAGCTCGTGAGCCGGTAGCTCCGCGCTACACTCCTGCGCCAGCATCAGGCAGTCGTCCGGCTG‑CCCCC‑TGGCCGAATGCGCAGCCAGGCTACCAGAAACAGCAAGGTGAAGTGTATCGCCAGCTTTTGCAAACGCCCGCGCCGATGCAAAAATTAAAAGCGCCGGAACCGCAGGAACCTGCACTTGCGGCGAA  >  NC_000913/4398434‑4398703

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A