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 F28 I0 R1 54 59.4 1320120 91.9% 1213190 218.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC NC_000913 1,619,080 Δ35 bp 12.0% intergenic (‑172/‑6) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 161907941 (0.770)6 (0.120) 6/402 NT 12.0% intergenic (‑171/‑41) marC/marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
?NC_000913 1619115 = 48 (0.930)intergenic (‑207/‑5) marC/marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance

GTTAGCTAACGGCAGCAACACCACCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1618849‑1619079
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggcaaCTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATG  >  NC_000913/1619115‑1619341
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
GTTAGCTAACGGCAGCAACACCACCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTATCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGG                                                                                                                                                                                                                                         >  2:35688/1‑227
   aaaggaaGGCAGCAAACCCCCCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAA                                                                                                                                                                                                                                     <  1:487218/221‑1
   AGCTAACGGCAGCAACACCACCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAA                                                                                                                                                                                                                                     >  2:589906/1‑228
                  CACCACCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTCCCTGGGCAACTAATGTGAAActg                                                                                                                                                                                                                       >  2:487218/1‑224
                               AGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCATTTCATTCATTTGACTTATACTTGCCTGGGCAACTAATGTGAAAAGTACCAGCGATCTTTT                                                                                                                                                                                                         >  1:60826/1‑228
                                                                                            AGCGAAAAGTTTAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTG                                                                                                                                            <  1:589906/228‑1
                                                                                            AGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGG                                                                                                                                                                                                                                         >  1:399031/1‑135
                                                                                             GCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGG                                                                                                                                                                                                                                        <  2:399031/135‑1
                                                                                                                           AGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGG                                                                                                                                                                                                                                         >  2:497746/1‑104
                                                                                                                            GTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGG                                                                                                                                                                                                                                        <  1:497746/104‑1
                                                                                                                                                             AACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAGTAAAGATCGCTTGCTTAACGCGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCG                                                                           >  2:641841/1‑228
                                                                                                                                                                    CTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCG                                                                    <  2:60826/228‑1
                                                                                                                                                                                                  GTCAATTCATTCATTTGACTTATACTTGCCTGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGAGATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCCCGGCGTGTATTACCCCGGTGTAACTGAAAAA                                       >  1:175578/1‑227
                                                                                                                                                                                                                                 GGGCCACTAATGGGAAAAGTACCCGCGAATTTGTCAATGAAATTATTCCATTGGGTCGCTTAACTCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCC       <  1:179491/228‑1
                                                                                                                                                                                                                                 GGGCACATAAGGTGAAAAGGTCCAGGGGTTTGTTCAAAGAAATTAATCCATGGGGCTGATTAAGCCTTATGGTTAATCAGAGTAAAGGTCGCCGGCTTAACGAGTATCTGTCTCCGCTGGATAGTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCC       <  1:186189/228‑1
                                                                                                                                                                                                                                      ACTAATGTGAAAAGGACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCGCCGCTGGATATTACCGCGGCTCAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATG  <  2:487414/228‑1
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
GTTAGCTAACGGCAGCAACACCACCAGCCCCAGGCCAATTGCTTTAAACAAATCTAACATTGGTGGTTGTTATCCTGTGTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1618849‑1619079
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggcaaCTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATG  >  NC_000913/1619115‑1619341

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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