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
A2 F27 I0 R1 83 86.1 2053078 89.1% 1829292 215.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,061,965 A→G 31.9% E56G (GAG→GGG)  torD → TorA‑maturation chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,061,9650AG31.9% 29.7 / 4.2 30E56G (GAG→GGG) torDTorA‑maturation chaperone
Reads supporting (aligned to +/- strand):  ref base A (13/6);  new base G (7/2);  total (22/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

GCGTTTAACGGCCCCGTGGAGATGGTGGCGCAGTGCGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGATCTATCTCGAATTGCT  >  NC_000913/1061734‑1062196
                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            
gtttttcccgcccctggggAGTTGGGGGTGCTGTGCATATTTGTCCCCGCGCCGATGGAAAAAATATGCCCACGCTGACGGCAAAAAAGTTGGCGTGTTTTTACCCCTGGCTAGCGCAGTTTTTCCCCGGGGAGCTGGACGATGAACAACTGACGCAAATCGCCGGTGTGCAGATGGCTAAATGGTTTTCGTGGCT‑AAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGaa                                                                                                                                                                                                                                      <  1:404207/222‑1 (MQ=255)
                             gcAGTGCGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGGG‑AACGGGCT‑GGAAAACCGTATTGCCCCGCTGCCAGTACGGGa                                                                                                                                                                                                         >  2:891201/1‑239 (MQ=255)
                                 tGCGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATAGCCAGTGGGCAGATGGCTGAATGGGTTTCGTTGCT‑GAAAAGAGAACCGCCGCTCACTGCGGCGGTGAAAGGAGCT‑GGAAAA‑CGTATTGCCACGcctacaattcggggacag                                                                                                                                                                                                     >  1:501479/1‑222 (MQ=255)
                                 tGCGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCCGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCCGTGCGCAGATGGCTGAATGGGTTTAGTTGCT‑GAAAAGCGAACCGCCGCTAACTGCGGCGGTG‑GAAGAGTTGGGAAAACCG‑ATTTCCAGGCTGAAAGTagggacacat                                                                                                                                                                                                     >  1:119704/1‑230 (MQ=255)
                                   cGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGGG‑AACGGGCT‑GGAAAACCGTATTGCACCGCTGACAGTACGTGACGATg                                                                                                                                                                                                    >  2:147298/1‑238 (MQ=255)
                                           ttCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGGTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGGG‑AACGGGCT‑GGAAAACCGGATTGCCACCCCGACAAGACGGGACGGAGCCCGGCT‑gg                                                                                                                                                                                          >  1:487869/1‑239 (MQ=255)
                                                   tCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGCCGGTT‑AACTGGCC‑GGGAAACCGGATTGCCCCGCTGACCACACGGGACGGT‑CCCCTCTGGGAACTggac                                                                                                                                                                                  >  2:466762/1‑237 (MQ=255)
                                                     gCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGGGCT‑GGAAAACCGTATTGCCACGCCGCCAGTACGTGACGATGCCCCTCT‑GGAACTGGcccc                                                                                                                                                                                >  2:669569/1‑237 (MQ=255)
                                                                                   caacaGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGGCT‑GGAACTGGCCCCGGGCTTTTGGGGCCCGTTTCTGATGACCg                                                                                                                                                   >  2:687337/1‑238 (MQ=255)
                                                                                         aTTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGCCTTTTTCGGCCTGTTTTTTATGACCGccaaaaa                                                                                                                                            >  1:985442/1‑237 (MQ=255)
                                                                                           tGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGGAAACCGTATTGCCACGCTGACAGGACGTGACGATGCCCGTCT‑GTAACTGGCCGCGGGCTTTTTGGGCCCGTTTTTGATGACGCacaaaaaaa                                                                                                                                          >  1:137095/1‑238 (MQ=255)
                                                                                           tGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAAACGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGGCTTTTTCGGCCTGTTTCTGATGACCGacaaacaaa                                                                                                                                          >  2:107763/1‑238 (MQ=255)
                                                                                                 tgtTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGGAAACCGTATTGCCACGCTGACAGACCGTGACGATGCCCGTCT‑GGGACTGGCCGCGGACTTTTGCGGCCGGTTTCTCATAACCGCCAAAAAAACGgggc                                                                                                                                    >  1:138051/1‑239 (MQ=255)
                                                                                                             gCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTgg                                                                                                                                                                                    >  2:877964/1‑179 (MQ=255)
                                                                                                                  cgcAGTTGTTATCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGGG‑AAAGAGCT‑GGAAAACCGGATTGCCACGCTGAACAAAAGTGACGAGGCCCGTCT‑GGAAATGGACGCGGGCTTTTGCGTCCCGGTTTGGAAGCCCGAGAAAAAAAGGGGGCGGCGGTATACAGCGGc                                                                                                                    >  1:917383/1‑238 (MQ=255)
                                                                                                                      gttgttCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGGATTGcc                                                                                                                                                                                                                          >  2:678805/1‑133 (MQ=255)
                                                                                                                       ttgttCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGa                                                                                                                                                                                                                                       >  2:948912/1‑119 (MQ=255)
                                                                                                                                     gctggagaagaaaaaatggacaaaaaTCGCAGGTGCGCAGATGGCTAAATGTTTTTCTTTGCG‑AAAAAGCAAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCaa                                                                                                <  2:985442/215‑1 (MQ=255)
                                                                                                                                         gACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGCGCT‑GGTAAACCGTATTGCGACCCTGACCGGACGTGACGCTGCCCGTCT‑GGGACTGGCCGCGGCCTTTTTCGGGCCCGTTCTTGTGACCGCCAAACAACAGGCGCGCCCGTATCCCTCTGccccacaaccggaccagaaaacgat                                                                                            >  1:618007/1‑216 (MQ=255)
                                                                                                                                              tGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACTGGCT‑GGAAAACCGCATTGCCACGCTGACCGGACGGCAAGGTGCACCGCC‑GCGACTGGCCGCAGGCATTTGCGCCGTTTTTCCGATTGCCCGCAAACACACCGACCCGGCGGGTGCATCGGCCCACAAAACAGGatagaaaagaattaaac                                                                                       >  1:994800/1‑223 (MQ=255)
                                                                                                                                               aaacaagTGACGAAACCCCCCAGGGCGAAG‑TGGGTGAATTGGTTTTGTTGGTAAAAAAGCAACCCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACg                                                                                     <  2:138051/238‑1 (MQ=255)
                                                                                                                                                             actccccAGGGGGCAGGTGGCTGATTGGTTTTCGTTGCG‑AAAAAGGCAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAgg                                                                      <  2:137095/234‑1 (MQ=255)
                                                                                                                                                             aaTCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACCGGCT‑GGAAAACCGGATTTCCACGCTGACAGTACGTGACGAATCCCGGCT‑GGAACTGGCCCCGGCCTTTTGCGGCCTGTTTTTCATGACCGCCAAACAACCCGCGCTCGCGTATGCCACGGCCCAC‑AAAACAGACGAGCAACAGATTAAACCCTttttgaggtggg                                                                       >  1:975677/1‑231 (MQ=255)
                                                                                                                                                                          cAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGAGTAAACCCTTGTTA‑GTTGAGGCAGGGGT‑GGgaa                                                         >  2:985951/1‑238 (MQ=255)
                                                                                                                                                                                                  cT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AAATTGCT‑CGAAAACCGTATTGCCACGCTGTCCGAACGTGAGGCTGACCCTCT‑GGAACGTGCCGCGGCCTTTTTAGGCCCGTTTCTGCTGAACGGTCAACAAACGGCGTCGCCGTATTGACCGGCCTTC‑AAACAGGATGAGACAAAGATTAAAAACCTGCTATGTTG‑GGCAGGGGTGGGAAACCA‑CGGCACTTTTAAAGaaacac                                 >  1:992451/1‑234 (MQ=255)
                                                                                                                                                                                                      gacgctctcccgccctctaCTGCGGCGGGC‑ACCGAGCT‑GGAAAGCCGTGTTGCCACCGTGGCGGTACGTGACCATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGGTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAg                              <  1:22289/220‑1 (MQ=255)
                                                                                                                                                                                                                  ctgcccagtGCGGCGGTT‑AACGAGGT‑GGAAAACCGTATAGCCAAGCTGACAGTAGGTGACGATGCCCGGCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGAAAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGat                 <  2:998142/231‑1 (MQ=255)
                                                                                                                                                                                                                       cACTGCGGCGGTG‑AACGGGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGatctatc            <  2:1853/239‑1 (MQ=255)
                                                                                                                                                                                                                             ggcggTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGAACAATCTCGAAt      >  2:318791/1‑239 (MQ=255)
                                                                                                                                                                                                                                  gg‑AACGGGCT‑GGAAAACCGTATGGCCACGCGGACAGTACGTGACGATGCCCGTCT‑GGAACGGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGATCTATCTCGAATTGCt  <  2:883842/237‑1 (MQ=255)
                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            
GCGTTTAACGGCCCCGTGGAGATGGTGGCGCAGTGCGAATATGTTCCCGCGTCGCAGGTGAAATCATGACCACGCTGACAGCACAACAGATTGCCTGTGTTTACGCCTGGCTAGCGCAGTTGTTCTCCCGTGAGCTGGACGATGAACAACTGACGCAAATCGCCAGTGCGCAGATGGCTGAATGGTTTTCGTTGCT‑GAAAAGCGAACCGCCGCTCACTGCGGCGGTG‑AACGAGCT‑GGAAAACCGTATTGCCACGCTGACAGTACGTGACGATGCCCGTCT‑GGAACTGGCCGCGGACTTTTGCGGCCTGTTTCTGATGACCGACAAACAAGCGGCGCTGCCGTATGCATCGGCCTAC‑AAACAGGACGAGCAAGAGATTAAACGCTTGTTA‑GTTGAGGCAGGGAT‑GGAAACCAGCGGCAATTTCAACGAACCGGCAGATCATCTGGCGATCTATCTCGAATTGCT  >  NC_000913/1061734‑1062196

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A