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
A13 F1 I1 R1 86 24.1 1002126 98.1% 983085 121.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,624,198 T→C pseudogene (312/351 nt) yrhC → pseudogene fragment

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,624,1980TC100.0% 33.0 / NA 10pseudogene (312/351 nt)yrhCpseudogene fragment
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/4);  total (6/4)

CGGGCAAATATAAATTTGCAAAAAATGCGAAGATAATGTTTTTAATATTTTGAACAATATGGCATTGAATGATAAGAGTGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGTTTTTTAT  >  NC_000913/3624120‑3624331
                                                                              |                                                                                                                                     
cGGGCAAATAAAAATTTGCAAAAAATGCGAAGATAATGTTTTTAATATTTTGAACAATATGGCATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCAc                                                                           >  2:22431/1‑139 (MQ=255)
   gCAAATAAAAATTTGCAAAAAATGCGAAGATAATGTTTTTAATATTTTGAACAATATGGCATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACttt                                                                        >  2:199203/1‑139 (MQ=255)
                                     gTTTTTAATATTTTGAACAATATGGCATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCATGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTaaaaa                                      <  1:18799/139‑1 (MQ=255)
                                          tAATATTTTGAACAATATGGCATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTgag                                 >  2:425108/1‑139 (MQ=255)
                                             tatTTTGAACAATATGGCATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGata                              <  1:22431/139‑1 (MQ=255)
                                                              cATTGAATGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAg             <  2:54965/139‑1 (MQ=255)
                                                                   aaTGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGtt        >  2:166470/1‑139 (MQ=255)
                                                                   aaTGATAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGtt        >  2:361402/1‑139 (MQ=255)
                                                                        tAAGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGTTTTTTa   <  1:425108/139‑1 (MQ=255)
                                                                         aaGAGCGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGTTTTTTAt  >  1:162133/1‑139 (MQ=255)
                                                                              |                                                                                                                                     
CGGGCAAATATAAATTTGCAAAAAATGCGAAGATAATGTTTTTAATATTTTGAACAATATGGCATTGAATGATAAGAGTGCTTGCGTTCGAGCTACGGCAATCGAGTCAACGGCCAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGTTTTTTAT  >  NC_000913/3624120‑3624331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A