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 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,609,336 (C)7→8 intergenic (+13/‑78) yjjG → / → prfC dUMP phosphatase/peptide chain release factor RF‑3

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,609,3291.C92.9% 41.3 / ‑2.8 14intergenic (+6/‑85)yjjG/prfCdUMP phosphatase/peptide chain release factor RF‑3
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (9/4);  total (10/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

TCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTG  >  NC_000913/4609242‑4609443
                                                                                         |                                                                                                                  
tCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcg                                                                  >  1:95667/1‑139 (MQ=255)
                    tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCCC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTCCTc                                              >  1:801738/1‑139 (MQ=255)
                     cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCa                                             >  1:17023/1‑139 (MQ=255)
                     cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCT‑c                                                                                                                   >  1:959282/1‑68 (MQ=255)
                     cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCT‑c                                                                                                                   <  2:959282/68‑1 (MQ=255)
                           cACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                       <  2:17023/139‑1 (MQ=255)
                                      tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAATAATTATGa                            >  2:689379/1‑139 (MQ=255)
                                      tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                            >  1:1024654/1‑139 (MQ=255)
                                      tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                            >  1:479214/1‑139 (MQ=255)
                                      tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                            >  1:64707/1‑139 (MQ=255)
                                        tcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                          <  2:64707/139‑1 (MQ=255)
                                               tGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCg                                                     >  1:920488/1‑105 (MQ=255)
                                               tGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCg                                                     <  2:920488/105‑1 (MQ=255)
                                                                cTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATg                                                        <  1:243198/85‑1 (MQ=255)
                                                                cTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATg                                                        >  2:243198/1‑85 (MQ=255)
                                                                cTCCTGTGTAAACACTGATTG‑CCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTg  >  1:550608/1‑139 (MQ=255)
                                                                                         |                                                                                                                  
TCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTG‑CCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTG  >  NC_000913/4609242‑4609443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A