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 F28 I1 R1 146 75.3 2562504 98.6% 2526628 139.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,643,053 T→C H27R (CAC→CGC)  rsmJ ← 16S rRNA m(2)G1516 methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,643,0530TC100.0% 145.1 / NA 39H27R (CAC→CGC) rsmJ16S rRNA m(2)G1516 methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/19);  total (20/19)

TGCGTCGGTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGTGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAGCATCGCATCCAGCTGCGGT  >  NC_000913/3642928‑3643185
                                                                                                                             |                                                                                                                                    
tGCGTCGGTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAg                                                                                                                        <  2:460202/140‑1 (MQ=255)
 gCGTCGGTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGc                                                                                                                       >  1:807570/1‑140 (MQ=255)
   gTCGGTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCgg                                                                                                                     <  1:817936/140‑1 (MQ=255)
       gTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGgccg                                                                                                                 <  2:1260709/140‑1 (MQ=255)
        tGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGgccgc                                                                                                                <  2:691739/140‑1 (MQ=255)
        tGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGgccgc                                                                                                                <  1:540110/140‑1 (MQ=255)
            ccATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGa                                                                                                            <  2:940424/140‑1 (MQ=255)
            ccATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGa                                                                                                            <  1:562949/140‑1 (MQ=255)
               tCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACa                                                                                                         >  2:541905/1‑140 (MQ=255)
                  cTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGAt                                                                                                      >  2:569517/1‑140 (MQ=255)
                           caaAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCg                                                                                             <  2:776151/140‑1 (MQ=255)
                                     aaaGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGc                                                                                   <  1:826073/140‑1 (MQ=255)
                                          tGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCCCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGTTAAGGCACCGCCCCCGGGCCCTGtt                                                                              >  2:450896/1‑140 (MQ=255)
                                                             atcaCGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGAttt                                                           >  1:520923/1‑140 (MQ=255)
                                                              tcaCGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGAtttt                                                          >  2:257397/1‑140 (MQ=255)
                                                               caCGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTc                                                         <  2:807570/140‑1 (MQ=255)
                                                               caCGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTc                                                         <  2:520923/140‑1 (MQ=255)
                                                                       cgcAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATg                                                 >  1:322525/1‑140 (MQ=255)
                                                                          aaTTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATc                                              <  2:749958/140‑1 (MQ=255)
                                                                                 gATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCtt                                       <  1:569517/140‑1 (MQ=255)
                                                                                     ttCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATg                                   <  2:847399/140‑1 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  2:765131/1‑140 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  1:1208096/1‑140 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  2:1219975/1‑140 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  1:798390/1‑140 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  1:450483/1‑140 (MQ=255)
                                                                                      tCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGc                                  >  1:362222/1‑140 (MQ=255)
                                                                                       ccGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGcc                                 >  1:956946/1‑140 (MQ=255)
                                                                                          gCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTa                              >  1:231510/1‑140 (MQ=255)
                                                                                           cGTTAACACCAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTaa                             <  2:1153157/140‑1 (MQ=255)
                                                                                                    cAGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAgc                    >  1:119731/1‑140 (MQ=255)
                                                                                                     aGCGCCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAgca                   <  1:765131/140‑1 (MQ=255)
                                                                                                       cgcCATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAgcatc                 <  2:362222/140‑1 (MQ=255)
                                                                                                          cATCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAgcatcgca              >  2:1201234/1‑140 (MQ=255)
                                                                                                            tCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTaa                             >  2:204072/1‑123 (MQ=255)
                                                                                                            tCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTaa                             <  1:204072/123‑1 (MQ=255)
                                                                                                            tCAGGTTGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAgcatcgcatc            >  2:213987/1‑140 (MQ=255)
                                                                                                                  tGTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAGCATCGCATCCAGCTg      <  2:119731/140‑1 (MQ=255)
                                                                                                                   gTCTTCATCGCGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAGCATCGCATCCAGCTGc     >  2:1013995/1‑140 (MQ=255)
                                                                                                                      ttCATCGCGCTCCAGCCCCCAGCAGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAGCATCGCATCCAGCTGCGGt  >  2:342635/1‑140 (MQ=255)
                                                                                                                             |                                                                                                                                    
TGCGTCGGTGCGCCATCGCTCCGCCAACAAAATCAACAAAGATGCCGCCAAGTTTTGGCTCATCACGCTTGCGCAATTCCAGATGTTCCGGCGTTAACACCAGCGCCATCAGGTTGTCTTCATCGTGCTCCAGCCCCCAGCGGGCCGCCAGAACAGATAAGGCACCGTCTCCGGTGCCTGTTTCATCAATTAAGCAGATTTTCACTGAATGATCAGCCCTTAATGCCGTAATGCTCCAGCATCGCATCCAGCTGCGGT  >  NC_000913/3642928‑3643185

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A