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
A13 F1 I2 R1 762 35.5 1545288 95.5% 1475750 117.0

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.C100.0% 60.9 / NA 18intergenic (+6/‑85)yjjG/prfCdUMP phosphatase/peptide chain release factor RF‑3
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (12/6);  total (12/6)

CAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTT  >  NC_000913/4609203‑4609459
                                                                                                                               |                                                                                                                                   
cAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccccccccgttg                                                                                                                        <  1:525665/139‑6 (MQ=255)
 aaCGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGa                                                                                                                        <  2:428891/139‑1 (MQ=255)
                                       tCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcg                                                                                  >  1:537377/1‑139 (MQ=255)
                                        cgcgAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgc                                                                                 >  1:645833/1‑139 (MQ=255)
                                                       ggCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccccccccgttg                                                                                                                        >  2:735228/1‑79 (MQ=255)
                                                       ggCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccccccccgttg                                                                                                                        <  1:735228/84‑6 (MQ=255)
                                                            cgcgCCCACCTGGACCGTTTCTTCGTTGCACGTACTGGAGCAGCTCCTGTGTAAACACGGATTGCCT‑‑cccccc                                                                                                                              <  1:468974/73‑1 (MQ=255)
                                                            cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑cccccc                                                                                                                              >  2:468974/1‑73 (MQ=255)
                                                                  cACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                       <  1:104363/139‑1 (MQ=255)
                                                                             tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                       <  1:643834/128‑1 (MQ=255)
                                                                             tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                       >  2:643834/1‑128 (MQ=255)
                                                                             tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                            >  1:361964/1‑139 (MQ=255)
                                                                             tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                            >  1:20132/1‑139 (MQ=255)
                                                                               tcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                          <  1:768436/139‑1 (MQ=255)
                                                                               tcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                          >  1:379519/1‑139 (MQ=255)
                                                                                                       cTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTg                  >  1:611863/1‑139 (MQ=255)
                                                                                                       cTCCTGTGTAAACACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTg                  >  2:627996/1‑139 (MQ=255)
                                                                                                       cTCCTGTGTAAACACTCATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTg                  >  1:249281/1‑139 (MQ=255)
                                                                                                                 agcacTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgcggcg                                                                             <  1:479973/68‑1 (MQ=255)
                                                                                                                 aaCACTGATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgcggcg                                                                             >  2:479973/1‑70 (MQ=255)
                                                                                                                    acTGATTGCCTCCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                          <  1:479256/103‑1 (MQ=255)
                                                                                                                    acTGATTGCCTCCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                          >  2:479256/1‑103 (MQ=255)
                                                                                                                       gATTGCCTC‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACtt  >  2:666959/1‑139 (MQ=255)
                                                                                                                               |                                                                                                                                   
CAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTT  >  NC_000913/4609203‑4609459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A