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
A1 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,259,458 G→A V64V (GTC→GTT)  tdcG ← L‑serine deaminase III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,259,4580GA100.0% 168.0 / NA 48V64V (GTC→GTT) tdcGL‑serine deaminase III
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/21);  total (27/21)

CTACAGGAAAATCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCGACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCC  >  NC_000913/3259322‑3259589
                                                                                                                                        |                                                                                                                                   
cTACAGGAAAATCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACa                                                                                                                                  >  1:559738/1‑140 (MQ=255)
   cAGGAAAATCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATcc                                                                                                                               >  1:626935/1‑140 (MQ=255)
     ggAAAATCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGt                                                                                                                             <  1:552631/140‑1 (MQ=255)
        aaaTCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGc                                                                                                                          >  1:474372/1‑140 (MQ=255)
         aaTCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCa                                                                                                                         <  1:716324/140‑1 (MQ=255)
               caaTATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGACATGGCCt                                                                                                                   <  2:640862/140‑1 (MQ=255)
                  tatGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTg                                                                                                                >  1:647861/1‑140 (MQ=255)
                    tGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGcc                                                                                                              >  1:541255/1‑140 (MQ=255)
                             gATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGa                                                                                                     >  2:183335/1‑140 (MQ=255)
                              aTGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGAc                                                                                                    >  1:857991/1‑140 (MQ=255)
                               tGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACa                                                                                                   <  1:95375/140‑1 (MQ=255)
                               tGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACa                                                                                                   <  2:857991/140‑1 (MQ=255)
                                   ccTGGAAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGa                                                                                               <  2:332547/139‑1 (MQ=255)
                                   aCTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGa                                                                                               <  2:510234/140‑1 (MQ=255)
                                   aCTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGa                                                                                               >  1:763868/1‑140 (MQ=255)
                                    cTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGAc                                                                                              <  2:748186/140‑1 (MQ=255)
                                     tGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGAcc                                                                                             <  1:561132/140‑1 (MQ=255)
                                        cAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGt                                                                                          >  1:10317/1‑140 (MQ=255)
                                            cgcccgcTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAg                                                                                      >  1:283044/1‑140 (MQ=255)
                                              cccgcTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGAt                                                                                    <  2:283044/140‑1 (MQ=255)
                                                    gcgcGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACca                                                                              <  1:183335/140‑1 (MQ=255)
                                                            cTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATgg                                                                      <  2:10317/140‑1 (MQ=255)
                                                                    ataAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTcgc                                                              >  1:876164/1‑140 (MQ=255)
                                                                    ataAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTcgc                                                              >  2:850210/1‑140 (MQ=255)
                                                                      aaaTGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCgg                                                            >  2:95305/1‑140 (MQ=255)
                                                                         tGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGGCGCGGttt                                                         >  2:697694/1‑139 (MQ=255)
                                                                           cAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTtaat                                                       >  1:274339/1‑140 (MQ=255)
                                                                           cAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGGtaat                                                       >  1:444193/1‑140 (MQ=255)
                                                                             gggATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTtaataa                                                     >  1:733969/1‑140 (MQ=255)
                                                                             gggATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCCCGGGtgataa                                                     >  1:510862/1‑140 (MQ=255)
                                                                                 tctcATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAg                                                    >  2:273565/1‑137 (MQ=255)
                                                                                 tctcATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAg                                                    <  1:273565/137‑1 (MQ=255)
                                                                                  ctcATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGc                                                >  1:515631/1‑140 (MQ=255)
                                                                                       caATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACtt                                           <  2:454524/140‑1 (MQ=255)
                                                                                        aaTGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACttt                                          >  1:197980/1‑140 (MQ=255)
                                                                                         aTGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTc                                         <  2:647861/140‑1 (MQ=255)
                                                                                            acaacaTCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGGTAATAAACCGCTACTTTCCaa                                      >  2:567694/1‑139 (MQ=255)
                                                                                               acaTCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCg                                   >  2:559842/1‑140 (MQ=255)
                                                                                                   ccTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCa                               >  1:794073/1‑140 (MQ=255)
                                                                                                           cTGTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACt                       >  2:33542/1‑140 (MQ=255)
                                                                                                             gTTTCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACttt                     <  2:541255/140‑1 (MQ=255)
                                                                                                              tttCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACtttt                    >  2:678378/1‑140 (MQ=255)
                                                                                                                tCCTGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTc                  <  2:763868/140‑1 (MQ=255)
                                                                                                                   tGCCAGTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCgg               <  1:95305/140‑1 (MQ=255)
                                                                                                                        gTCCCATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCCACTTTCCCGCCGAACAATAAAAATTTTTTCCGcattt          >  2:444895/1‑139 (MQ=255)
                                                                                                                          cccATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGcattcat        <  2:559738/140‑1 (MQ=255)
                                                                                                                           ccATGATGATGGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGcattcatt       <  2:794073/140‑1 (MQ=255)
                                                                                                                                atgatgGCAACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGccc  <  2:293678/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                   
CTACAGGAAAATCAACAATATGCGCACCAGATGCCACTGGCAGCCGCCCGCTGCGCGTTACTAACTCTATAAATGCAGGGATCTCATCAATGACAACATCCTGCGGACTGTTTCCTGCCAGTCCCATGATGATGGCGACATCCGTGGCATGGCCTTTGCCCGTCAGTGACAACGACCCGTACAGATCGACCACAATATGGCTCGTCGCGGTTAATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCC  >  NC_000913/3259322‑3259589

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