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
A8 F1 I1 R1 82 28.6 1225488 97.4% 1193625 116.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,128,620 A→G T117A (ACG→GCG)  glcC → glycolate‑inducible glc operon transcriptional repressor, autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,128,6200AG96.3% 94.4 / ‑4.0 27T117A (ACG→GCG) glcCglycolate‑inducible glc operon transcriptional repressor, autorepressor
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (13/13);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

TCGCACGGCTTAATCGGGTGCAGGACACCAGCCCGCTGATCCATCTGTTCAGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAACGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCTTTCCATCTCGCCATTTGTCAGG  >  NC_000913/3128483‑3128749
                                                                                                                                         |                                                                                                                                 
tCGCACGGCTTAATCGGGTGCAGGACACCAGCCCGCTGATCCATCTGTTCAGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAAc                                                                                                                                  <  1:39590/139‑1 (MQ=255)
              cGGGTGCAGGACACCAGCCCGCTGATCCATCTGTTCAGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTttg                                                                                                                    <  2:58314/139‑1 (MQ=255)
                               cccGCTGATCCATCTGTTCAGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGt                                                                                                   >  2:430767/1‑139 (MQ=255)
                                                  aGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTcgccg                                                                                <  1:2818/139‑1 (MQ=255)
                                                         aGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCa                                                                             <  1:387627/135‑1 (MQ=255)
                                                         aGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCAGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCa                                                                             >  2:387627/1‑135 (MQ=255)
                                                                   gCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACaaa                                                               <  1:282600/139‑1 (MQ=255)
                                                                             cTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGc                                                     >  2:83820/1‑139 (MQ=255)
                                                                               gCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTgaga                                                                       >  1:585142/1‑119 (MQ=255)
                                                                               gCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTgaga                                                                       <  2:585142/119‑1 (MQ=255)
                                                                                    aCGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGa                                              <  2:217009/139‑1 (MQ=255)
                                                                                      gTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCt                                                                                     <  1:3611/98‑1 (MQ=255)
                                                                                      gTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCt                                                                                     >  2:3611/1‑98 (MQ=255)
                                                                                      gTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAAc                                            >  1:457512/1‑139 (MQ=255)
                                                                                         cgcgCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATg                                         <  1:169789/139‑1 (MQ=255)
                                                                                          gcgcATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGa                                              <  1:317912/133‑1 (MQ=255)
                                                                                          gcgcATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGa                                              >  2:317912/1‑133 (MQ=255)
                                                                                                      aGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCa                            >  1:518746/1‑139 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTcgc                                                                                  >  1:111014/1‑81 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTcgc                                                                                  <  2:111014/81‑1 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCt                        >  1:74499/1‑139 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCt                        >  1:512332/1‑139 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCt                        >  1:480250/1‑139 (MQ=255)
                                                                                                          cGAATCGGCAAGGCTGGCGGCAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCAGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCt                        >  1:101469/1‑139 (MQ=255)
                                                                                                                            ggcAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCTTTCCATCTCGCCATTTGt      <  1:83820/139‑1 (MQ=255)
                                                                                                                             gcAACGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCTTTCCATCTCGCCATTTGTc     <  2:101469/139‑1 (MQ=255)
                                                                                                                                aCGCTGGGAGCGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCTTTCCATCTCGCCATTTGTCAgg  <  2:480250/139‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                 
TCGCACGGCTTAATCGGGTGCAGGACACCAGCCCGCTGATCCATCTGTTCAGTACGCAGCCGCGAACGCTGTACGATCTGCTCGACGTTCGCGCATTACTGGAGGGCGAATCGGCAAGGCTGGCGGCAACGCTGGGAACGCAGGCTGATTTTGTTGTGATAACCCGCTGTTATGAAAAAATGCTCGCCGCCAGTGAGAACAACAAAGAGATTTCGCTGATCGAACATGCGCAGTTGGATCACGCTTTCCATCTCGCCATTTGTCAGG  >  NC_000913/3128483‑3128749

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