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
A6 F17 I0 R1 19 52.5 1051376 98.5% 1035605 229.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,782,916 G→A 22.8% L249L (CTG→TTG)  gpsA ← glycerol‑3‑phosphate dehydrogenase (NAD+)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,782,9160GA22.8% 25.4 / 2.2 26L249L (CTG→TTG) gpsAglycerol‑3‑phosphate dehydrogenase (NAD+)
Reads supporting (aligned to +/- strand):  ref base G (4/16);  new base A (4/2);  total (8/18)
Fisher's exact test for biased strand distribution p-value = 5.10e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAATGCTGCCTCGCGCGCGTTTTTTCCGCAATATAATACTTGATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAAACGCGGAAACTTTTGCCG  >  NC_000913/3782685‑3783142
                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                   
tCAATGCTGCCTCGCGCGCGTTTTTTCCGCAATATAATACTTGATAGATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGCCTGGTTTGCGGG‑ACAGGTAAGGACCAGATCCCCa                                                                                                                                                                                                                              >  1:328121/1‑239 (MQ=255)
    tgctgcCTCGCGCGCGTTTTTTCCGCAATATAATACTTGATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGCCTTGTTGTCGGG‑AAAGGTAAACACCAGAACCCCAAGc                                                                                                                                                                                                                           >  1:492692/1‑238 (MQ=255)
    tgctgcCTCGCGCGCGTTTTTTCCGCAATATAATACTTGATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACCCGACCGGTTGGCGGT‑ACAGGTAAGCACCAACTCGCCCAGc                                                                                                                                                                                                                           >  1:26543/1‑238 (MQ=255)
       tgcCTCGCGCGTGTTTTTTCCGAAATACAATACTGGAGAAATTCCCTCGGTTATGGGCAGTTCACCGACGAGGCGATGCGCCAGTCCGCGGACTTCTTGCGTATTGCGGTAGCCTTCCACCCCCGGAACAATCTCCTCCTCCGCGCTTTGTACACCCATTCCCTGACCGAGCTACATCCCAAAACGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGAACGCCACGCCCCg                                                                                                                                                                                                                       <  2:451974/239‑1 (MQ=255)
           gcggcggggTTTTTCCCGCAATTTAAAGCTTGTAAAATTTCCTCGGTTTTTGGCATTTCACCGCCAAAGCGATGCGCCGGTTCGCGGTCTTCTTTCGTATTGGGGTAGCCTCCCCCCACCTGCCCAATCTTCCCCTGCGCGCTTTGTACACCCAGGCCCTGACCGAGCCTCATGCCAAAACGGCGGTTACGGGACTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCAt                                                                                                                                                                                                                   <  2:336391/231‑1 (MQ=255)
                          ccGCATTATAATACTTGATAAATTTCCCCGGTTATTGGCATTTCACCGCCGAAGCGATGCGCCATTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCCCCCCCTGACCAATCTCCTCCTGCGCGCTTTGTACATCCATGCCCTGACGGGGCATCATGCCAAACCGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAGGCACCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGc                                                                                                                                                                                                   <  2:76340/239‑1 (MQ=255)
                                        ttGATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGACTGGTTGTCGGG‑ACAGGTAAGCACCAGATCGCCAAACCCCGCCATGCCCCT‑AAAAGTGGCAGGGTCGGCAccc                                                                                                                                                                                      >  1:323323/1‑238 (MQ=255)
                                          gATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCCACCGGTTTTCGGTGACA‑GTAAACACCAAAACGCCAAACCCCCCCCTGCCCAC‑AAAGGTGGGAGGGGGGGCAccccc                                                                                                                                                                                    >  2:503202/1‑236 (MQ=255)
                                            tAAATTTCCTCGGTTATTGCCATTTCAACGCCGAAGCGATGCGCCATTTCGCGGACTTCTTTCGTTGTGCGGTACCCTCCCCCCCCCGGACCATTCTTCTCCTGCGCGTTTTGTCCATCCATGCCCTGACCGAGCATCAGGCCAAACCGGCGGTTACGCGACTGTTTGTCGGT‑ACAGGTAAGCCCCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAgcg                                                                                                                                                                                  <  2:20682/238‑1 (MQ=255)
                                                      cGGTTGTTGGCATTTCACCGCCGAGGCGCGCCGCCATTCCGCGGACTCCTTTCGTATTGCGGTACCCTCCCGCCACCTGCCCAATCTTCCCCTCCGCGCTTTGTACACCAAGGCCCTGACCGACCATCATCCCAAACCGGCGGTTACGCGCGTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCAAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGa                                                                                                                                                                       <  2:183205/239‑1 (MQ=255)
                                                          tATTGGCATGACAGCGCGGACGCGAGGCGCCGGTTCGCGGACTTCTTTCGTATTGGGGTAGCCTTCCACCCCCGGACCACTCTTCTCCTGCGCGCTTTGTACATCCATGCCCGGACCGGGCATCAGGCCAAAACGGCGGTTACGCGATTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGAcgcg                                                                                                                                                                   <  2:227356/239‑1 (MQ=255)
                                                                           cGAAGCGGTGCGCCCGTTCGCGGACTTCTTTCGTAGTGCGTGAGCCTTCCACCACTTGACCAATCTTCCCCTGCGCGCTTTGTCCATCCATGCCCTGACGGGGCATCATGCCAAAACGGCGGTTACGCGACTGGTGGTCGGT‑ACAGGTAAGCACCAGAGCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCa                                                                                                                                                  <  2:71146/239‑1 (MQ=255)
                                                                                      gcCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGGGCATCAGGCCAAACCGGCGGTTCCGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAg                                                                                                                                       <  2:432990/239‑1 (MQ=255)
                                                                                      gcCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCGGACCAATCTCCTCCTGCGCGCTTTGTACGTCCATGCCCTGACCGAGCATCGCGCCAAAACGGCGGTTCCGCGACTGGTTGGCGGT‑CCAGGTAAGCACCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAg                                                                                                                                       <  2:757/239‑1 (MQ=255)
                                                                                                                    tggCCTTCCCCCCCCTGACCAATTTTCTCCGGCGCGTTTTGTAATCCCATGCCCTGACCGAGCATCATGCAAAACCGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGa                                                                                                          <  2:492692/236‑1 (MQ=255)
                                                                                                                                    gcccAATCTTCTCCGGCGCGTTTTGTACATCCAGGCCCTGACCGAGCCTCACGCCAAAACGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATcccc                                                                                         <  2:166419/237‑1 (MQ=255)
                                                                                                                                                      cgcTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGACTGGGTGTCGGG‑ACAGGGAAGCACCAAAACCCCAAGCCCCCCCCTGCCCCT‑AAAGGGGGCAGGGGCGGCACCCCGCGCCGCCCCCAGACGCCACCATTTAGCCCACCCACCGGGGAACAGCGCCCTACGCGCAATCCCCCCCAAACCCACACCCCCGGACATCCCCCCCCCACTCGCCATaaac                                                                       >  2:47707/1‑237 (MQ=255)
                                                                                                                                                                  ccACGCCCTGACCGAGCATCAGGCCAAAACGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGACCCCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACcgcg                                                           <  1:6649/239‑1 (MQ=255)
                                                                                                                                                                     tGCCCTGACCGAGCATCATGCCAAAACGGCGGTTAACCGACTGGGTGTCGGG‑AAAGGGAAAGACCAAAACGCCAAGCCCCCCCCTGCCCCTAAAAGGGGGAAGGGCGGGCA‑CCAGAGCCCCCCCCACAAGCGACACTTCAGCCAACCCACCGGGGGTCCGCGCCCCCCCCGCCTTCCCCACAAAACCCACACCCTCGGACCTCCCCCCCCCACCGGCACACACGTGTTTCCCCGcccc                                                         >  2:233421/1‑238 (MQ=255)
                                                                                                                                                                        catgcccGAGCATCAGGCAAAAACGGTGGTGACGCGACTGGTTGCCGGT‑ACGGGAAAGCACCAGAACGCCAGGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCa                                                     <  2:304193/234‑1 (MQ=255)
                                                                                                                                                                                          aaaaaCGGCGGTCACGCGACTGGTTGCCGGT‑ACAGGTAAGCACCAGACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGaa                                    <  1:144246/237‑1 (MQ=255)
                                                                                                                                                                                                ggcagTTACGCGATGGGTTGTCGGT‑ACTGGAAAGCCCCAAACCGCCCAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCTCCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGa                             <  1:350953/239‑1 (MQ=255)
                                                                                                                                                                                                                   gTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCACCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAAACGCGGaa            >  1:61180/1‑237 (MQ=255)
                                                                                                                                                                                                                          ccggttgaGCACCAAACCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGGGATCAGCCCCGTACGCGCATTCGCACCAAATCCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAAACGCGGAAACTTTTg     <  1:158293/231‑1 (MQ=255)
                                                                                                                                                                                                                             ggaaaGCCCCGGACCGCAAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAGACGCGGAAACTTTTGCCg  <  2:327211/235‑1 (MQ=255)
                                                                                                                                                                                                                              gTAACCACCAGACCGCAAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAAACGCGGAAACTTTTGCCg  <  2:323323/237‑1 (MQ=255)
                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                   
TCAATGCTGCCTCGCGCGCGTTTTTTCCGCAATATAATACTTGATAAATTTCCTCGGTTATTGGCATTTCAACGCCGAAGCGATGCGCCAGTTCGCGGACTTCTTTCGTATTGCGGTAGCCTTCCACCACCTGACCAATCTTCTCCTGCGCGCTTTGTACATCCATGCCCTGACCGAGCATCATGCCAAAACGGCGGTTACGCGACTGGTTGTCGGT‑ACAGGTAAGCACCAGATCGCCAAGCCCCGCCATGCCCAT‑AAAGGTGGCAGGGTCGGCACCCAGCGCCGCACCAAGACGCGACATTTCAGCCAGCCCACGGGTGATCAGCGCCGTACGCGCATTCGCACCAAAACCGATACCGTCGGACATCCCCGCACCAATGGCAATAACGTTTTTCACCGCGCCGCCAAGCTGCACGCCAATGAAATCCGGATTGCTGTAAACGCGGAAACTTTTGCCG  >  NC_000913/3782685‑3783142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A