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 I211 R1 223 18.0 1007644 96.3% 970361 85.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 592,895 A→C L103F (TTA→TTC)  cusF → Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273592,8950AC100.0% 28.9 / NA 10L103F (TTA→TTC) cusFCu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (3/7);  total (3/7)

ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC  >  NZ_CP009273/592809‑592976
                                                                                      |                                                                                 
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg                                                                                <  1:453233/90‑1 (MQ=255)
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg                                                                                <  2:496253/90‑1 (MQ=255)
       cGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg                                                                                <  1:98605/83‑1 (MQ=255)
       cGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg                                                                                >  2:98605/1‑83 (MQ=255)
              gAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAg                                                                  <  2:83696/90‑1 (MQ=255)
                        gAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAAccc                                                        <  1:245488/90‑1 (MQ=255)
                                    ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCNTTAACCCAGTTTTAATtag                                            >  1:108339/1‑90 (MQ=255)
                                                 cGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATcg                               <  1:124303/90‑1 (MQ=255)
                                                                 gcagGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGgcag               >  2:458496/1‑90 (MQ=255)
                                                                              tctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggc  <  2:410127/90‑1 (MQ=255)
                                                                                      |                                                                                 
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC  >  NZ_CP009273/592809‑592976

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTAT  >  NZ_CP009273/592809‑592957
                                                                                      |                                                              
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG                                                   <  SRR3722094.100030/100‑1 (MQ=60)
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG                                                   <  SRR3722094.461209/100‑1 (MQ=60)
                        GAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATG                           <  SRR3722094.249043/100‑1 (MQ=60)
                          AATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCNTTAACCCAGTTTTAATTAG                         >  SRR3722094.109898/1‑100 (MQ=60)
                                                 CGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTAT  <  SRR3722094.126087/100‑1 (MQ=60)
                                                                                      |                                                              
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTAT  >  NZ_CP009273/592809‑592957

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑