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 I210 R1 226 19.6 1130256 95.4% 1078264 84.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,897,230 A→G D309G (GAT→GGT)  manX → PTS mannose transporter subunit IIAB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,897,2300AG100.0% 84.0 / NA 26D309G (GAT→GGT) manXPTS mannose transporter subunit IIAB
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (13/13);  total (13/13)

TATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTC  >  NZ_CP009273/1897165‑1897316
                                                                 |                                                                                      
tatCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat                                                                      <  2:487284/84‑1 (MQ=255)
tatCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat                                                                      >  1:487284/1‑84 (MQ=255)
         gTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaa                                                       >  1:31735/1‑90 (MQ=255)
         gTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaa                                                       <  1:541099/90‑1 (MQ=255)
         gTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaa                                                       >  2:255559/1‑90 (MQ=255)
                 aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa                                               <  2:210296/90‑1 (MQ=255)
                      aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa                                          <  2:169145/90‑1 (MQ=255)
                        tGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACg                                        <  2:331017/90‑1 (MQ=255)
                           gcgcgGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa                                          >  1:283451/1‑85 (MQ=255)
                           gcgcgGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa                                          <  2:283451/85‑1 (MQ=255)
                           gcgcgGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAt                                     >  2:309/1‑90 (MQ=255)
                               ggTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATtgtg                                 >  2:395517/1‑90 (MQ=255)
                                gTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTgtgt                                <  2:31735/90‑1 (MQ=255)
                                          ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAg                                             <  1:256190/67‑1 (MQ=255)
                                          ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAg                                             >  2:256190/1‑67 (MQ=255)
                                          ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa                                          >  1:212640/1‑70 (MQ=255)
                                          ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa                                          <  2:212640/70‑1 (MQ=255)
                                          ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc                      >  1:158470/1‑90 (MQ=255)
                                               tCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGt                 >  1:84149/1‑90 (MQ=255)
                                                ccGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAt                                     >  1:369594/1‑69 (MQ=255)
                                                ccGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAt                                     <  2:369594/69‑1 (MQ=255)
                                                     aGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTcac           <  2:158470/90‑1 (MQ=255)
                                                        tttCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa                                               >  1:409131/1‑51 (MQ=255)
                                                        tttCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa                                               <  2:409131/51‑1 (MQ=255)
                                                          tCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTa      >  2:53919/1‑90 (MQ=255)
                                                              ccGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTc  <  1:255559/90‑1 (MQ=255)
                                                                 |                                                                                      
TATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTC  >  NZ_CP009273/1897165‑1897316

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTACGTAAAC  >  NZ_CP009273/1897132‑1897326
                                                                                                  |                                                                                                
GGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGT                                                                                                 >  SRR3722092.178093/1‑100 (MQ=60)
                       ATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCT                                                                          >  SRR3722092.496967/1‑100 (MQ=60)
                                ATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAA                                                                 >  SRR3722092.32285/1‑100 (MQ=60)
                                          GTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAG                                                       <  SRR3722092.551963/100‑1 (MQ=60)
                                                  AACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAT                                               >  SRR3722092.288337/1‑100 (MQ=60)
                                                    gtataagagacaGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTG                                             <  SRR3722092.260367/88‑1 (MQ=60)
                                                                 GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTctgtctctta                                >  SRR3722092.216143/1‑90 (MQ=60)
                                                                 GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC                                >  SRR3722092.161118/1‑100 (MQ=60)
                                                                      GAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGT                           >  SRR3722092.85602/1‑100 (MQ=60)
                                                                       AGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTctgtcgcttat                          >  SRR3722092.376537/1‑89 (MQ=60)
                                                                               GTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATctgtctcttatacacatctgacgctgccg                  >  SRR3722092.417020/1‑71 (MQ=60)
                                                                                               CCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTACGTAAAC  <  SRR3722092.259723/100‑1 (MQ=60)
                                                                                                  |                                                                                                
GGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTACGTAAAC  >  NZ_CP009273/1897132‑1897326

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑