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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG  >  NZ_CP009273/3786373‑3786551
                                                                                              |                                                                                    
ATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGA                                                                                 >  SRR3722077.288139/1‑100 (MQ=60)
ATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGA                                                                                 >  SRR3722077.234193/1‑100 (MQ=60)
                      ATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGA                                                           <  SRR3722077.277804/100‑1 (MQ=60)
                          ATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTG                                                       >  SRR3722077.88276/1‑100 (MQ=60)
                          ATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTG                                                       >  SRR3722077.770599/1‑100 (MQ=60)
                                  ccgtgggtctcgtgggctcggagatgtgtataagagacagAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAG                                               <  SRR3722077.743420/60‑1 (MQ=60)
                                       CATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTT                                          >  SRR3722077.588718/1‑100 (MQ=60)
                                       CATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTT                                          >  SRR3722077.1008265/1‑100 (MQ=60)
                                         TTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTT                                        >  SRR3722077.331713/1‑100 (MQ=60)
                                          TTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTT                                       <  SRR3722077.1018309/100‑1 (MQ=60)
                                              ctcggagatgtgtataagagacagCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTAT                                   <  SRR3722077.20909/76‑1 (MQ=60)
                                                gggctcggagatgtgtataagagacagATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAG                                 <  SRR3722077.693258/73‑1 (MQ=60)
                                                        agatgtgtataagagacagATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGA                         <  SRR3722077.180279/81‑1 (MQ=60)
                                                          CAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATG                       >  SRR3722077.1158180/1‑100 (MQ=60)
                                                           AATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGC                      <  SRR3722077.723428/100‑1 (MQ=60)
                                                               GCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCT                  <  SRR3722077.134119/100‑1 (MQ=60)
                                                                  CCCCCAATAATATATACATGATTGCCGATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTAC               >  SRR3722077.1056453/1‑100 (MQ=60)
                                                                     CCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTT            >  SRR3722077.137363/1‑100 (MQ=60)
                                                                      CAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTC           >  SRR3722077.1153865/1‑100 (MQ=60)
                                                                      CAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTC           >  SRR3722077.1049678/1‑100 (MQ=60)
                                                                        ATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCAT         >  SRR3722077.716496/1‑100 (MQ=60)
                                                                        ATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCAT         >  SRR3722077.375969/1‑100 (MQ=60)
                                                                          AATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGActgtctcttatacacatc       >  SRR3722077.657904/1‑82 (MQ=60)
                                                                          AATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCA       >  SRR3722077.851887/1‑100 (MQ=60)
                                                                           ATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAA      >  SRR3722077.407528/1‑100 (MQ=60)
                                                                            TATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAA     >  SRR3722077.620118/1‑100 (MQ=60)
                                                                             ATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGActgtctcttatacacatctcc    >  SRR3722077.440168/1‑79 (MQ=60)
                                                                             ATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAT    >  SRR3722077.78099/1‑100 (MQ=60)
                                                                             ATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAT    >  SRR3722077.140487/1‑100 (MQ=60)
                                                                               ATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG  >  SRR3722077.4937/1‑100 (MQ=60)
                                                                                              |                                                                                    
ATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG  >  NZ_CP009273/3786373‑3786551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑