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 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,031,991 Δ1 bp coding (327/1419 nt) dcm ← DNA cytosine methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,031,9910C.100.0% 161.9 / NA 39coding (327/1419 nt)dcmDNA cytosine methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (23/16);  total (23/16)

ACGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCACTGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCTTT  >  NC_000913/2031863‑2032122
                                                                                                                                |                                                                                                                                   
acGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAAt                                                                                                                          >  2:310066/1‑139 (MQ=255)
                tGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGa                                                                                                          <  1:753132/139‑1 (MQ=255)
                  aGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACg                                                                                                        >  2:86060/1‑139 (MQ=255)
                  aGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACg                                                                                                        >  2:307648/1‑139 (MQ=255)
                             gcgGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCg                                                                                                                               <  2:717108/105‑1 (MQ=255)
                             gcgGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCg                                                                                                                               >  1:717108/1‑105 (MQ=255)
                                     cTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCg                                                                                     >  2:392561/1‑139 (MQ=255)
                                       tCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGaa                                                                                   <  1:307648/139‑1 (MQ=255)
                                                     cGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCTCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGc                                                                     >  2:8009/1‑139 (MQ=255)
                                                      gTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCg                                                                    <  1:86060/139‑1 (MQ=255)
                                                                        tGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGgatg                                                  >  2:505806/1‑139 (MQ=255)
                                                                          gTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGgatgat                                                >  2:1037461/1‑139 (MQ=255)
                                                                             ggCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATa                                                                                 <  1:91387/103‑1 (MQ=255)
                                                                             ggCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATa                                                                                 >  2:91387/1‑103 (MQ=255)
                                                                             ggCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGAtgtg                                             >  2:658869/1‑139 (MQ=255)
                                                                             ggCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGAtgtg                                             >  1:267502/1‑139 (MQ=255)
                                                                               cTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGaa                                                                                   >  2:925524/1‑99 (MQ=255)
                                                                               cTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGaa                                                                                   <  1:925524/99‑1 (MQ=255)
                                                                                       gTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGttt                                   <  1:505806/139‑1 (MQ=255)
                                                                                         gCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTgg                                 >  1:718849/1‑139 (MQ=255)
                                                                                          cGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                        <  2:559087/83‑1 (MQ=255)
                                                                                          cGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                        >  1:559087/1‑83 (MQ=255)
                                                                                            tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGaa                                                                  <  1:1023268/103‑1 (MQ=255)
                                                                                            tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGaa                                                                  >  2:1023268/1‑103 (MQ=255)
                                                                                                       tgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGc                   >  1:928768/1‑139 (MQ=255)
                                                                                                         ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGa                                                                                                          >  2:1069579/1‑50 (MQ=38)
                                                                                                         ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGa                                                                                                          <  1:1069579/50‑1 (MQ=38)
                                                                                                          tCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGa                <  1:1037461/139‑1 (MQ=255)
                                                                                                              ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGa                                                                   <  1:917342/84‑1 (MQ=255)
                                                                                                              ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGa                                                                   >  2:917342/1‑84 (MQ=255)
                                                                                                              ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATggg            >  2:234527/1‑139 (MQ=255)
                                                                                                              ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATggg            >  2:1027209/1‑139 (MQ=255)
                                                                                                              ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATggg            >  1:447582/1‑139 (MQ=255)
                                                                                                               tCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGc           >  2:506243/1‑139 (MQ=255)
                                                                                                                cGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCg          <  1:43850/139‑1 (MQ=255)
                                                                                                                 gCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGa         >  1:311404/1‑139 (MQ=255)
                                                                                                                   tGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAAc       <  1:785702/139‑1 (MQ=255)
                                                                                                                        aaCACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCttt  <  1:69426/139‑1 (MQ=255)
                                                                                                                        aaCACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCttt  <  1:310066/139‑1 (MQ=255)
                                                                                                                                |                                                                                                                                   
ACGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCACTGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCTTT  >  NC_000913/2031863‑2032122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A