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
CGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAAC  >  NZ_CP009273/661796‑661974
                                                                                                |                                                                                  
CGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCG                                                                                 <  SRR3722077.419725/100‑1 (MQ=60)
      taagagacagGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCC                                                                           <  SRR3722077.202520/90‑1 (MQ=60)
           gccggcatacgagatggccgtgggtctcgtgggctcggagatgtgtataagagacagTCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAAT                                                                      <  SRR3722077.236008/43‑1 (MQ=60)
           CCGCAGGCAGATCGGTGTTGTTATCCCCCAGCATAATGTGGCCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAAT                                                                      <  SRR3722077.662417/100‑1 (MQ=60)
                              GTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGC                                                   <  SRR3722077.190648/100‑1 (MQ=60)
                              GTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGC                                                   >  SRR3722077.450164/1‑100 (MQ=60)
                                TATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGG                                                 <  SRR3722077.34543/100‑1 (MQ=60)
                                   CACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATT                                              >  SRR3722077.432918/1‑100 (MQ=60)
                                     CCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGT                                            <  SRR3722077.909528/100‑1 (MQ=60)
                                            TAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG                                     <  SRR3722077.830266/100‑1 (MQ=60)
                                            TAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG                                     <  SRR3722077.1096051/100‑1 (MQ=60)
                                              ATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCG                                   >  SRR3722077.284772/1‑100 (MQ=60)
                                               agagacaGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGC                                  <  SRR3722077.192126/93‑1 (MQ=60)
                                                    TGGAGGATCTGGGGCTTCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGG                             <  SRR3722077.526995/100‑1 (MQ=60)
                                                         GATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTC                        <  SRR3722077.1103552/100‑1 (MQ=60)
                                                              GGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAG                   >  SRR3722077.785809/1‑100 (MQ=60)
                                                               GCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGT                  <  SRR3722077.890999/100‑1 (MQ=60)
                                                                    TCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTG             >  SRR3722077.1094400/1‑100 (MQ=60)
                                                                      AGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGT           <  SRR3722077.753874/100‑1 (MQ=60)
                                                                      AGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGT           <  SRR3722077.239370/100‑1 (MQ=60)
                                                                         GTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCAC        >  SRR3722077.342548/1‑100 (MQ=60)
                                                                               ACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAAC  <  SRR3722077.341750/100‑1 (MQ=60)
                                                                               ACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAAC  <  SRR3722077.1026799/100‑1 (MQ=60)
                                                                                                |                                                                                  
CGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAAC  >  NZ_CP009273/661796‑661974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑