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
A6 F80 I0 R1 1105 125.4 6144758 94.6% 5812941 133.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC NC_002947 4,978,181 Δ9 bp 25.0% coding (456‑464/696 nt) flgH ← flagellar L‑ring protein

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 = 497818085 (0.740)29 (0.250) 25/244 NT 25.0% coding (465/696 nt) flgH flagellar L‑ring protein
?NC_002947 4978190 = 89 (0.780)coding (455/696 nt) flgH flagellar L‑ring protein

CGGCCACACGGGTGGACGGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4978047‑4978180
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACGGATTATTGGTGTTGGGCGT  >  NC_002947/4978190‑4978329
                                                                                                                                                                                                                                                                                  
CGGCCACACGGGTGGACGGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGG                                                                                                                              <  1:2511914/150‑1
  GCCAGACGGGTGGACGGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTG                                                                                                                            <  2:564577/150‑1
                 GGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAAC                                                                                                                     <  1:1185906/142‑1
                 GGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAAC                                                                                                                     >  2:1185906/1‑142
                                         TCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTG                                                                                     <  2:2986339/150‑1
                                                        ATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCG                                                                      >  1:1298248/1‑150
                                                        ATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCG                                                                      >  1:466206/1‑150
                                                              GCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGGTCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTG                                                                            >  1:2039831/1‑138
                                                              GCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTG                                                                            <  2:2039831/138‑1
                                                                       ACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGGTCGCCGCTATAA                                                       >  2:2892475/1‑150
                                                                       ACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAA                                                       >  1:2111412/1‑150
                                                                       ACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATC                                                                                                                         <  1:3051544/84‑1
                                                                       ACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATC                                                                                                                         >  2:3051544/1‑84
                                                                         CAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGAT                                                                                                                          >  2:1332722/1‑81
                                                                         CAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGAT                                                                                                                          <  1:1332722/81‑1
                                                                           GCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGC                                                                       >  1:2152361/1‑130
                                                                           GCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGC                                                                       <  2:2152361/130‑1
                                                                             TCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCC                                                 <  2:64729/150‑1
                                                                               TTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTC                                               >  1:816178/1‑150
                                                                                              GGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACC                                >  1:339132/1‑150
                                                                                                TCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGC                              <  1:1160254/150‑1
                                                                                                    CCACTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACGGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGAACGCCGCTATAACCGGCCTCCAGCGAAAGATCACCGCCACC                          >  2:1180306/1‑150
                                                                                                       CTTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAA                       <  2:816178/150‑1
                                                                                                        tcaTCGCCGTGCGCGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAAC                      >  1:572684/4‑150
                                                                                                        TTCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAAC                      <  1:1850344/150‑1
                                                                                                         TCTCGCCGCGCACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACG                     >  2:2559120/1‑150
                                                                                                                   CACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACGGATTATT              >  2:241949/1‑147
                                                                                                                   CACGGCGATGATGCCGTTGTCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACGGATTATT              <  1:241949/147‑1
                                                                                                                            GATGCCGTTGTCGGCCACGGTGACGGTGATCGAACTGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACGGATTATTGGTGTTGGGCGT  <  1:292462/150‑1
                                                                                                                                                                                                                                                                                  
CGGCCACACGGGTGGACGGCACGGTGTTGTCGGTGGCGATATCGTCAGCGCGAACCATGCCGGCAATGCGCACCAGCTCTTCGCCGGTGTTCAGGGTCAGCCACTTCTCGCCGCGCACGGCGATGATGCCGTTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4978047‑4978180
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCCACGGTGACGGTGATCGAACCGGTCAGCGTGTTGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGGTCACCGCCACCGAACGGATTATTGGTGTTGGGCGT  >  NC_002947/4978190‑4978329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A