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 I229 R1 214 17.4 943020 97.5% 919444 87.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,060,988 (A)6→5 intergenic (+240/‑53) yccE → / → agp YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,060,9830A.100.0% 14.4 / NA 5intergenic (+235/‑58)yccE/agpYccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (2/3);  total (2/3)

GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAG  >  NZ_CP009273/1060916‑1061029
                                                                   |                                              
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac                         <  1:57475/90‑1 (MQ=255)
         tGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtg                >  2:224141/1‑90 (MQ=255)
             gATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattg            <  2:458547/90‑1 (MQ=255)
                gTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATa         <  1:396922/90‑1 (MQ=255)
                       gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGCCATATTTCTATCACACTCTTTAGTGATTGATAACAAAag  >  2:295690/1‑90 (MQ=255)
                                                                   |                                              
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAG  >  NZ_CP009273/1060916‑1061029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ 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
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGG  >  NZ_CP009273/1060916‑1061075
                                                                        |                                                                                       
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGA                                                             <  SRR3722113.57974/100‑1 (MQ=60)
                GTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGG                                             <  SRR3722113.401071/100‑1 (MQ=60)
                                                           GTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATTAACAAAACGCTAATCGCCGCAGCTGTGGCAGG  >  SRR3722113.402135/1‑100 (MQ=60)
                                                                        |                                                                                       
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGG  >  NZ_CP009273/1060916‑1061075

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑