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
A16 F28 I0 R1 2812 90.9 3266724 96.2% 3142588 148.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,708,758 G→C 54.7% E614Q (GAA→CAA)  rsxC → SoxR [2Fe‑2S] reducing system protein RsxC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,708,7580GC54.7% ‑6.6 / 9.5 11E614Q (GAA→CAA) rsxCSoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand):  ref base G (3/2);  new base C (2/4);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 5.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-01

CCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCC  >  NC_000913/1708609‑1708904
                                                                                                                                                     |                                                                                                                                                  
cccGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAAGCAGAACAACAGGGCGATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCagaag                                                                                                                                                    <  1:1294160/150‑1 (MQ=255)
                                       ataacgAAGCAGAACCACAGGATGATCCTCGCAAACCCGCCGTCGAAGCAGCTATTGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTa                                                                                                             <  1:1561769/145‑1 (MQ=14)
                                                                      cAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGAGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTCGATCCGAGCAACGACGACGTCGAAGCCGCTATTGCCAGTGCAAAAGCACGCAAGCGGGAACa                                                                              >  2:1494670/1‑150 (MQ=14)
                                                                                                cccGTGAAAAATCTCGCAAGCAGGAACAGCAACAGGATAATCCGGAAGCAGAACAACAGGTCGATCCCCGCAAACCCGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaac                                                    <  1:1469556/150‑1 (MQ=11)
                                                                                                      ccAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTg                                                                                                    <  1:206030/96‑1 (MQ=33)
                                                                                                      ccAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTg                                                                                                    >  2:206030/1‑96 (MQ=33)
                                                                                                                  aGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCa                                  >  1:950521/1‑150 (MQ=255)
                                                                                                                              aaCAGGCTAATGCGCAACCAGAACACCCGGGCGCTCCGCGCAACGCCGCCGTCGACGCCGCTATAGCCCGTGCCAACGCACGCAAGCGGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCg                      <  1:1231344/150‑1 (MQ=11)
                                                                                                                                          cGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGa                                                            <  1:1548593/100‑1 (MQ=18)
                                                                                                                                          cGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGa                                                            >  2:1548593/1‑100 (MQ=18)
                                                                                                                                                cAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGa                                                      >  1:1548910/1‑100 (MQ=37)
                                                                                                                                                cAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGa                                                      <  2:1548910/100‑1 (MQ=37)
                                                                                                                                                  gaagaaCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAAGCAAATGCCTAGCCAGAAAAACAGGTCGATCCGCGCAAAGCCGCAGTCGAAGCAGCTATTGACCGAGca  >  2:592628/1‑149 (MQ=14)
                                                                                                                                                  gaagaaCAGGTCGATCCGCGCAAAGCCGCAGTCGAAGCCGATATTGCCCGAGACAAAGCACGCAAGATGGAAAAGCAAAAGGCTAATGCCGAGCCAGAACAACAGGTAGATCCGCGCAAAGCCGCAGTCGAAGCCGGTATTGACGGAGcc  >  2:1269155/1‑150 (MQ=14)
                                                                                                                                                     |                                                                                                                                                  
CCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCC  >  NC_000913/1708609‑1708904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A