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
A10 F1 I2 R1 757 38.1 1607544 96.5% 1551279 117.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,709,163 T→C S8P (TCC→CCC)  rsxD → SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,709,1630TC92.9% 42.5 / ‑6.0 14S8P (TCC→CCC) rsxDSoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (6/7);  minor base A (1/0);  total (7/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGG  >  NC_000913/1709028‑1709295
                                                                                                                                       |                                                                                                                                    
gCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCcccc                                                                                                                                   >  2:263321/1‑139 (MQ=255)
    aTGCGGCACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTta                                                                                                                               <  1:71286/139‑1 (MQ=255)
        ggTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCACCCCTTATAcc                                                                                                                           >  2:520379/1‑139 (MQ=255)
          tACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCa                                                                                                                         >  2:281724/1‑139 (MQ=255)
               gaagaaCAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATAccc                                                                                                                          >  1:497307/1‑133 (MQ=255)
               gaagaaCAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATAccc                                                                                                                          <  2:497307/133‑1 (MQ=255)
                             tCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATcg                                                                                                      >  1:184444/1‑139 (MQ=255)
                                       gCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGc                                                                                            <  2:565614/139‑1 (MQ=255)
                                                         aTTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                          <  1:263321/139‑1 (MQ=255)
                                                                                               ggTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTttggt                                    <  1:409658/139‑1 (MQ=255)
                                                                                                    tAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTgggg                               >  2:211244/1‑139 (MQ=255)
                                                                                                        cGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTAct                           <  2:184444/139‑1 (MQ=255)
                                                                                                                 aaTGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAg                  >  2:346529/1‑139 (MQ=255)
                                                                                                                      tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCa                                                                                                  <  1:798198/54‑1 (MQ=255)
                                                                                                                      tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCa                                                                                                  >  2:798198/1‑54 (MQ=255)
                                                                                                                                agctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCg   >  2:445912/1‑139 (MQ=255)
                                                                                                                                 gctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCgg  <  1:520379/139‑1 (MQ=255)
                                                                                                                                  ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCAt                                                                                                 <  2:392236/43‑1 (MQ=255)
                                                                                                                                  ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCAt                                                                                                 >  1:392236/1‑43 (MQ=255)
                                                                                                                                       |                                                                                                                                    
GCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGG  >  NC_000913/1709028‑1709295

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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