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
A30 F999 I0 R1 5 5.1 414173 44.8% 185549 128.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,810 Δ1 bp intergenic (‑42/+53) pyrE ← / ← rph orotate phosphoribosyltransferase/truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8090G.85.7% 11.1 / ‑3.9 7intergenic (‑41/+54)pyrE/rphorotate phosphoribosyltransferase/truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base . (3/3);  minor base C (1/0);  total (4/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

GCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGC  >  NC_000913/3815696‑3815911
                                                                                                                 |                                                                                                      
gCGTAAACTCGCCAAACTTTAACACCGGCTTGCTAAGCCCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGc                                                                                        <  1:202898/129‑1 (MQ=255)
          gCCAAAATTTAAACCCTGTTGTCCAAATGCAAATTCAATAAACTGGCGCTTAAATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATc                                                                              <  1:158625/129‑1 (MQ=255)
             aaaCTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCGCATCTTACTTTTCTACAGCCAAAAAAAA‑GCGACTCATACGTCGCCTTAAAAATCa                                                                             >  1:344486/1‑127 (MQ=255)
                                                 aaaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTTTGCGTCGTTCCAAGGgatt                                       >  1:189521/1‑129 (MQ=255)
                                                        cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGCCAAAAAAAACG‑GCCTCATCAGTCCCCTTAAAAA‑CAGTTTTCCCACGCCCCCCTCTTGGTCGCTACAAAGGATTCGATTccc                               >  1:136029/1‑129 (MQ=255)
                                                                                 ccctcAACTTTCTTTTCCAACGACAAAAAAAA‑GCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGa       <  1:162811/128‑1 (MQ=255)
                                                                                      aTCTTACTTTTCTACAGACAAAAAAAA‑GCGACTCATCAGTCGCCTTCAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCCGGGCCAGAGCCCAAAAAATGAGTAGc  >  1:97067/1‑129 (MQ=255)
                                                                                                                 |                                                                                                      
GCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGC  >  NC_000913/3815696‑3815911

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A