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 F3 I122 R1 193 20.9 1228102 94.7% 1163012 84.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 4,117,071 T→C F44S (TTC→TCC)  rpmE → 50S ribosomal protein L31

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,117,0710TC100.0% 36.3 / NA 11F44S (TTC→TCC) rpmE50S ribosomal protein L31
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/7);  total (4/7)

CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGA  >  NZ_CP009273/4116985‑4117155
                                                                                      |                                                                                    
ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                                   <  1:192033/90‑1 (MQ=255)
  gctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTg                                                                                 >  2:569299/1‑90 (MQ=255)
        gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                           <  2:427981/90‑1 (MQ=255)
                         aTCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTAcc                                                          >  2:241545/1‑90 (MQ=255)
                            cGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGt                                                       <  2:239153/90‑1 (MQ=255)
                                        ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                           <  2:155001/90‑1 (MQ=255)
                                                   gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                                <  2:479911/90‑1 (MQ=255)
                                                               gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACAt                    >  1:4905/1‑90 (MQ=255)
                                                                      aaGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgc             <  1:141978/90‑1 (MQ=255)
                                                                        gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag           <  1:269826/90‑1 (MQ=255)
                                                                                 gTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGa  >  2:68616/1‑90 (MQ=255)
                                                                                      |                                                                                    
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGA  >  NZ_CP009273/4116985‑4117155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC  >  NZ_CP009273/4116985‑4117156
                                                                                      |                                                                                     
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAG                                                                          <  SRR3721989.195544/100‑1 (MQ=60)
                                                     ACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACAT                     >  SRR3721989.4994/1‑100 (MQ=60)
                                                                      AAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAG    <  SRR3721989.144561/100‑1 (MQ=60)
                                                                        GTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC  <  SRR3721989.274633/100‑1 (MQ=60)
                                                                                      |                                                                                     
CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC  >  NZ_CP009273/4116985‑4117156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑