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 F4 I96 R1 227 23.3 882352 98.0% 864704 126.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 579,220 T→A N28K (AAT→AAA)  appY → DNA‑binding transcriptional activator AppY

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273579,2200TA100.0% 23.4 / NA 7N28K (AAT→AAA) appYDNA‑binding transcriptional activator AppY
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (4/3);  total (4/3)

ACTACTATCAACTTGTTTTAATTTTATGATAGGTGCAAGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAATTCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTG  >  NZ_CP009273/579098‑579347
                                                                                                                          |                                                                                                                               
actactATCAACTTGTTTTAATTTTATGATAGGTGCAAGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGt                                                                                                                   >  2:184624/1‑137 (MQ=255)
                        tATGATAGGTGCAAGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTa                                                                                          <  2:28778/138‑1 (MQ=255)
                                      gATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCctct                                                                           <  1:184624/139‑1 (MQ=255)
                                               tGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGa                                                                  <  1:169301/139‑1 (MQ=255)
                                                    gCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAAttgt                                                             >  1:132390/1‑139 (MQ=255)
                                                                                                  gagaGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAATATGTTTATCCTTTTTTATCGACGTGaa                >  2:123019/1‑138 (MQ=255)
                                                                                                               ttCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTg  >  1:71574/1‑139 (MQ=255)
                                                                                                                          |                                                                                                                               
ACTACTATCAACTTGTTTTAATTTTATGATAGGTGCAAGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAATTCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTG  >  NZ_CP009273/579098‑579347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAATTCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTGG  >  NZ_CP009273/579135‑579348
                                                                                     |                                                                                                                                
AGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAAT                                                                 <  SRR3722119.186543/151‑1 (MQ=60)
    GGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTT                                                             >  SRR3722119.133741/1‑151 (MQ=60)
         ATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATAT                                                        <  SRR3722119.171047/151‑1 (MQ=60)
                                                               GAGTTATCTCGTTCAAAAAAAAATCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTGG  >  SRR3722119.72268/1‑151 (MQ=60)
                                                                                     |                                                                                                                                
AGATGGATTATGTTTGCTCCGTAGTTTTCATCTGTCAATCATTTGATTTAATTATAAACAGGAGAGTTATCTCGTTCAAAAAAAATTCATTGTTTATTGTAAGCGACAAAATTAGAAGGGAGTTACCAGTATGCCCCTCTAAACTAAGAATTGTTGATATAGATAAGAAAACATGTTTATCCTTTTTTATCGACGTGAATAATGAGCTGCCTGG  >  NZ_CP009273/579135‑579348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑