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 F2 I75 R1 71 32.8 2150506 93.3% 2006422 83.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,841,981 (C)6→5 coding (285/1044 nt) selD ← selenide, water dikinase SelD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,841,9760C.100.0% 80.9 / NA 20coding (290/1044 nt)selDselenide, water dikinase SelD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (9/11);  total (9/11)

TCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGCCCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATA  >  NZ_CP009273/1841898‑1842056
                                                                              |                                                                                
tCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGcccccatc                                                                           >  1:693123/1‑83 (MQ=255)
tCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGcccccatc                                                                           <  2:693123/86‑4 (MQ=255)
  ggTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAg                                                                    >  2:133565/1‑90 (MQ=255)
       cTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATc                                                               >  2:877574/1‑90 (MQ=255)
             gggCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGAt                                                         <  2:43202/90‑1 (MQ=255)
                  aTTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGt                                                    <  2:401723/90‑1 (MQ=255)
                      cTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGt                                                <  1:514893/90‑1 (MQ=255)
                          ggAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGAGAAGATATCGATGATGGCGTTAGTcgcc                                            >  1:149159/1‑90 (MQ=255)
                                         cGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCaaaa                             >  1:460184/1‑90 (MQ=255)
                                               gCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGaaa                       <  2:729981/90‑1 (MQ=255)
                                               gCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGaaa                       <  2:384313/90‑1 (MQ=255)
                                                ccGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAg                      <  1:68482/90‑1 (MQ=255)
                                                    ggATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGAtt                  >  2:500402/1‑90 (MQ=255)
                                                         gCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCaa             >  2:901118/1‑90 (MQ=255)
                                                         gCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCaa             >  1:1065786/1‑90 (MQ=255)
                                                         gCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCaa             >  2:45786/1‑90 (MQ=255)
                                                         gCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCaa             >  2:351789/1‑90 (MQ=255)
                                                             tCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGAt         <  1:901118/90‑1 (MQ=255)
                                                              cGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATc        <  2:408710/90‑1 (MQ=255)
                                                              cGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATc        <  1:460573/90‑1 (MQ=255)
                                                                ccATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCgg      <  1:133565/90‑1 (MQ=255)
                                                                    aaTCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATa  <  2:829842/90‑1 (MQ=255)
                                                                              |                                                                                
TCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGCCCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATA  >  NZ_CP009273/1841898‑1842056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATAGCGTCCACCTTCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGCCCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTA  >  NZ_CP009273/1841885‑1842071
                                                                                                |                                                                                          
ATAGCGTCCACCTTCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCG                                                                                        <  SRR3722213.851028/100‑1 (MQ=60)
   GCGTCCACCTTCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGA                                                                                     >  SRR3722213.708702/1‑100 (MQ=60)
                             CAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGAGAAGATATCGATGATGGCGTTAGTCGCC                                                           >  SRR3722213.152532/1‑100 (MQ=60)
                                   CTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATG                                                     <  SRR3722213.526496/100‑1 (MQ=60)
                                            GTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAA                                            >  SRR3722213.470563/1‑100 (MQ=60)
                                                            GCCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAA                            >  SRR3722213.1089304/1‑100 (MQ=60)
                                                             CCGAGGATCGCAATCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAAC                           <  SRR3722213.70032/100‑1 (MQ=60)
                                                                          TCGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAG              <  SRR3722213.920908/100‑1 (MQ=60)
                                                                           CGCCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGA             <  SRR3722213.470966/100‑1 (MQ=60)
                                                                             CCATAATCGGTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAG           <  SRR3722213.136607/100‑1 (MQ=60)
                                                                                      GTTTG‑CCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTA  >  SRR3722213.602839/1‑100 (MQ=60)
                                                                                                |                                                                                          
ATAGCGTCCACCTTCGGTCACTTCGCGGGCAATTTCTGGGGAAAGTTTGTTAATCGGCCAGCCGAGGATCGCAATCGCCATAATCGGTTTGCCCCCCATCGCGAAGATATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTA  >  NZ_CP009273/1841885‑1842071

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑