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 I228 R1 214 26.5 1448192 97.1% 1406194 86.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,240,670 Δ1 bp coding (55/441 nt) BW25113_RS06225 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,240,6670G.100.0% 28.4 / NA 8coding (52/441 nt)BW25113_RS06225hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (4/4);  total (4/4)

ATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACC  >  NZ_CP009273/1240582‑1240750
                                                                                     |                                                                                   
aTCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATgggcg                                                                                 >  2:248355/1‑88 (MQ=255)
          aaTTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAgg                                                                      <  2:556764/90‑1 (MQ=255)
                      gttgttTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTg                                                          >  2:298203/1‑90 (MQ=255)
                                 tgtgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa                                               <  1:505636/90‑1 (MQ=255)
                                   tgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTTTTTAACa                                             >  2:372726/1‑90 (MQ=255)
                                          gAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTTAAAATTTAGaa                                      >  2:270759/1‑90 (MQ=255)
                                                              gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAg                  >  2:95649/1‑90 (MQ=255)
                                                                      tCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGcc          <  2:93019/90‑1 (MQ=255)
                                                                              tAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATAcc  <  1:428092/90‑1 (MQ=255)
                                                                                     |                                                                                   
ATCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACC  >  NZ_CP009273/1240582‑1240750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ 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
TGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATG  >  NZ_CP009273/1240615‑1240762
                                                       |                                                                                            
TGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAT                                                 <  SRR3722112.512991/100‑1 (MQ=60)
                                             TAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAA    <  SRR3722112.433854/100‑1 (MQ=60)
                                               AAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTATTTAACATTTAGAATTTATCAATCCTTCTGGCAGATTAAGCCAAAAAACCCGTTCGGCAATG  >  SRR3722112.666052/1‑100 (MQ=60)
                                                       |                                                                                            
TGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATG  >  NZ_CP009273/1240615‑1240762

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑