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
A12 F28 I1 R1 123 51.0 1731148 99.3% 1719029 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,977,215 (A)8→7 intergenic (‑76/+51) motA ← / ← flhC motility protein A/DNA‑binding transcriptional dual regulator FlhC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,977,2080A.100.0% 218.0 / NA 51intergenic (‑69/+58)motA/flhCmotility protein A/DNA‑binding transcriptional dual regulator FlhC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (24/27);  total (24/27)

CACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTT  >  NC_000913/1977073‑1977343
                                                                                                                                       |                                                                                                                                       
cACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGCaaaaa                                                                                                                                     <  1:771258/140‑1 (MQ=255)
      tcatcaAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGCaaaaaaagcag                                                                                                                               >  1:67920/1‑136 (MQ=255)
      tcaccaAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGCaaaaaaagcag                                                                                                                               <  1:491966/140‑5 (MQ=255)
          caAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGt                                                                                                                          >  1:138961/1‑140 (MQ=255)
                    ccgAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTAc                                                                                                                <  2:337396/140‑1 (MQ=255)
                      gAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCg                                                                                                              <  1:502319/140‑1 (MQ=255)
                         aaCTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACAACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCgctg                                                                                                           <  1:285157/140‑1 (MQ=255)
                            tGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGctgctg                                                                                                        >  1:572022/1‑140 (MQ=255)
                              tACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGa                                                                                                      >  1:842402/1‑140 (MQ=255)
                                   agaACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGtt                                                                                                 >  2:628708/1‑140 (MQ=255)
                                      acaacCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTgcg                                                                                              >  2:99247/1‑140 (MQ=255)
                                       caacCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTgcgc                                                                                             <  1:400223/140‑1 (MQ=255)
                                        aacCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGcc                                                                                            >  2:374735/1‑140 (MQ=255)
                                         acCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCt                                                                                           <  2:265930/140‑1 (MQ=255)
                                         acCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCt                                                                                           <  1:293819/140‑1 (MQ=255)
                                           cAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCa                                                                                         <  2:842402/140‑1 (MQ=255)
                                               tAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGt                                                                                     <  1:374735/140‑1 (MQ=255)
                                                  ccTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATc                                                                                  >  2:766847/1‑140 (MQ=255)
                                                  ccTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATc                                                                                  >  2:409391/1‑140 (MQ=255)
                                                         agataagCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTaaa                                                                           <  2:67920/140‑1 (MQ=255)
                                                             aagCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGc                                                                       <  1:409391/140‑1 (MQ=255)
                                                                cACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGc                                                                       >  1:377125/1‑137 (MQ=255)
                                                                cACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGc                                                                       <  2:377125/137‑1 (MQ=255)
                                                                  cGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTa                                                                  <  2:707444/140‑1 (MQ=255)
                                                                     catcatCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAg                                                                        >  2:97808/1‑131 (MQ=255)
                                                                     catcatCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAg                                                                        <  1:97808/131‑1 (MQ=255)
                                                                     catcatCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTActc                                                               >  1:212320/1‑140 (MQ=255)
                                                                     catcatCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTActc                                                               >  2:829952/1‑140 (MQ=255)
                                                                               ccACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTAct                                                                >  1:276491/1‑129 (MQ=255)
                                                                               ccACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTAct                                                                <  2:276491/129‑1 (MQ=255)
                                                                               ccACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATc                                                     >  1:4910/1‑140 (MQ=255)
                                                                                  cTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcag                                                  <  2:138961/140‑1 (MQ=255)
                                                                                  cTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcag                                                  <  1:284261/140‑1 (MQ=255)
                                                                                  cTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcag                                                  <  2:696236/140‑1 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               <  1:99247/140‑1 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               >  1:523982/1‑140 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               >  1:42718/1‑140 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               >  2:526352/1‑140 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               >  1:142337/1‑140 (MQ=255)
                                                                                     ttGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGAGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCcagcag                                               >  1:394417/1‑140 (MQ=255)
                                                                                        aCCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTtg                                            <  2:572022/140‑1 (MQ=255)
                                                                                          cATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTtgtg                                          >  1:799133/1‑140 (MQ=255)
                                                                                                 ggATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGataat                                   <  2:394417/140‑1 (MQ=255)
                                                                                                  gATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGataata                                  >  1:656727/1‑140 (MQ=255)
                                                                                                      ttCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCgg                              >  2:716980/1‑140 (MQ=255)
                                                                                                       tCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGc                             >  1:546523/1‑140 (MQ=255)
                                                                                                       tCAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGc                             <  2:799133/140‑1 (MQ=255)
                                                                                                        cAGTCGTCAGGCGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCa                            <  1:700552/140‑1 (MQ=255)
                                                                                                                   cGTTAACGCGCGATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGa                 <  2:142337/140‑1 (MQ=255)
                                                                                                                         cgcgcgATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTc                      >  2:599377/1‑129 (MQ=255)
                                                                                                                         cgcgcgATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTc                      <  1:599377/129‑1 (MQ=255)
                                                                                                                          gcgcgATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTa          <  1:766847/140‑1 (MQ=255)
                                                                                                                            gcgATTGGGGC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACg        <  1:253916/140‑1 (MQ=255)
                                                                                                                                  ggggC‑AAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCtttt  <  2:42718/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CACCGGTCATCAAATAACCGCCGAAAACTGTACCGAGAACAACCAGGTAACCTAATAAGATAAGCACGACATCATCCTTCCACTGTTGACCATGACAGGATGTTCAGTCGTCAGGCGTTAACGCGCGATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTT  >  NC_000913/1977073‑1977343

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