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
A3 F28 I0 R1 54 59.4 1320120 91.9% 1213190 218.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 954,374 C→G 37.3% P31P (CCG→CCC)  focA ← formate channel

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913954,3740CG37.3% 9.0 / 4.9 30P31P (CCG→CCC) focAformate channel
Reads supporting (aligned to +/- strand):  ref base C (11/5);  new base G (2/9);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.83e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

TGCGCCCACTCGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATA  >  NC_000913/954154‑954589
                                                                                                                                                                                                                                       |                                                                                                                                                                                                                        
tGCGCCCACTCGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCGGTGAT‑ATAG‑AAAACGAATGCGATTGAGATGAAAACACCGCCGGTAATTGCC‑CAAT‑GG‑AAAGACTTAA‑TCGGAGGtt                                                                                                                                                                                                                   >  2:290095/1‑228 (MQ=255)
      cACTCGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGGT‑AG‑AAAGCATTAA‑ACGGATGtttgcttg                                                                                                                                                                                                             >  2:70687/1‑223 (MQ=255)
        cTCGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑CGGA‑TG‑AAAAACTTAA‑ACGGAGGATTCGTTGc                                                                                                                                                                                                            >  2:99348/1‑227 (MQ=255)
          cGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCACGAACAAGTTTTGCCATTCCG‑AAGGGCATTGT‑GCCTCGG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAAGTGGATTGAGATGAAAACACCGGCGGTAATCTGC‑AAGT‑GG‑AAAGCATTAA‑GGGGGGGTTTCGtgtgtt                                                                                                                                                                                                          >  2:74414/1‑222 (MQ=255)
            ccTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAATCTTAA‑GCGGATGTTTCGTTTCtttc                                                                                                                                                                                                        >  2:244140/1‑226 (MQ=255)
                               cacGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGGAAACACCGGCGGTAATTGCC‑AGAT‑AG‑AAAGACTTAA‑GCGGATGGTTCGTTGGTTTATATACAACCCCCCCTTCTG‑c                                                                                                                                                                                   >  2:74154/1‑228 (MQ=255)
                                   gTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAAGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGGGAT‑ATAG‑AAGACGAATGCGATTGAGATTAAAACACCGGCGGTAATCGCC‑AGAA‑AG‑AAAGTCTTTA‑GCGGGTGTTACGTTGGTTTATAAACACCCCCCCCCTCGG‑cccat                                                                                                                                                                               >  2:483950/1‑225 (MQ=255)
                                            aaGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATGGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGGATTAA‑ACGGAGGTTTTGTTGGTTTATAAACACCCCCCCCTTTGG‑CCACTTTGGCCCtt                                                                                                                                                                      >  2:207747/1‑228 (MQ=255)
                                                    ggCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGA‑GCCTGTG‑CCAGGGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑CGAT‑AG‑AAAGACTTAA‑AAGGCTGGTTCGTTGCTTTTTATAAACACGCCCCTTCTG‑CCACTTTGTGCATTgtagactg                                                                                                                                                              >  1:492620/1‑224 (MQ=255)
                                                    gcctccgaaactaacaAAACGAATCAGCCCAAGAATGAAG‑AAGTGCCCGCCACCCATTTGCGACGGGCCG‑AGGGGAAGTGT‑GCC‑GTG‑GCCTTGGCTTGCTGTGAT‑AAAG‑AAGACAAATGAGATGGAAAGTAAACCACGGGGGTAAACCGCC‑AGAT‑AG‑AACCTGTTAT‑GGGGTTTTTCGGTTTTTTTATAGACCCCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAgg                                                                                                                                                              <  1:126679/216‑1 (MQ=255)
                                                      cTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGGTGAAAAAACCGGCGGTAAACGCC‑AGGT‑AG‑AAAGCATTAA‑GAGGAGGTTTCGTTGGTTTTTAGAAAACCCCCCCTTCGGCCCCCTTTGGCCTTTgacacggaa                                                                                                                                                             >  1:508555/1‑220 (MQ=255)
                                                             aaaaacaCAAAGAATCAGCCCCAGAGGGAAGCAAATG‑CCGCAAACCGGTTTTGCCAGGACG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATGTTTCGTTGCTTTATAGACACCCGCCTCCTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTaaaa                                                                                                                                                      <  1:244140/224‑1 (MQ=255)
                                                                aacaCAAAGAATCACCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCAATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATACCC‑CGCT‑CG‑AAAAGCCTAC‑ACGGATGTTTCTCTTCGTCATAAACACACCCCCCCTCCG‑ACACTTTGTCCATTTGCGCAGGAATAaaaatgaa                                                                                                                                                  >  1:352527/1‑224 (MQ=255)
                                                                   acaAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑ACGGAGGTTTCGTGGCTTTATAACCACCCGCCCCTTCGG‑CCACTTTGGCCCtttctgaggggataaaaaaaacaa                                                                                                                                                >  1:499310/1‑205 (MQ=255)
                                                                           tcgaccacAGGGAGAAGCATATC‑CCGCCAACAAGTTGTGACTTGCC‑‑AAGGGGAATGG‑GGCTGGGTAGAGTGG‑TTGTTATGAA‑AGAG‑AAGAGTAATGCTTTTGGGTGGAAACCACCGTCGTTAACCGCC‑TTAT‑AG‑AAAGTCTTAA‑GCGGATGTTTGGTTCTTTTATAAAAACTCGCCTCTTCGG‑CCCCTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGt                                                                                                                                       <  2:324801/221‑1 (MQ=255)
                                                                                  gggagagaAAC‑AAGG‑CCCCCAACCTGTTTTTGCAACGCG‑AGGGGGTTTGTGGCCGGTG‑CCGGTGG‑TGGCTGTAAA‑AAAA‑AAAAGAAAGGGGTTTGAGGATAAAACCCGGGCGGTAATCCAC‑AAAA‑AA‑AAAGTTTTAG‑GGGGTTTTTTCGTTTCTTTAAAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCttt                                                                                                                                <  1:406481/226‑1 (MQ=255)
                                                                                   agagagAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGAATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATTGTC‑CGAA‑AGAAAAGACTTAG‑GGGGA‑GTGTCTTTGCTTTATAGAAACCCCCCCCTTCGG‑ACACTTTGGCCAATGTAGCAGGAAATaaaaaaaccacaagtgtgtacggtg                                                                                                                                 >  1:324801/1‑205 (MQ=255)
                                                                                             caatatgcccccctattttttTCCATGCCGAAAGTGTATTTG‑GACTGTG‑CGAGTGG‑TTG‑GGTGATAAAAG‑AACAGGATTCGTATGGGGCTGAACACCCAGACGGTAATCGCA‑AGAT‑AA‑AAGTTCTAAA‑GGGGGTTTTTCGTTGCTTTATAAACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTGCACACTAAc                                                                                                                       <  1:222402/211‑1 (MQ=255)
                                                                                                 gcccgcaAACAAGTTTTGCCATGCGG‑AAGGGATTTGG‑CCCGGTG‑CCAGTGT‑TTGGTGTAAT‑ATAA‑AAGACGAATGCGATTGAGATAAAACCCCCGGGGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATGTTTCTTTGCTTTATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAActctc                                                                                                                   <  2:508555/225‑1 (MQ=255)
                                                                                                                        gccgggggcgaTTGT‑GCCTTGG‑CTAGTTG‑TTGTTG‑GAA‑AAAGAAAAACGAATGGTGTTGAAATGAAAACCCGGGGGGTACTCGCC‑AGAG‑AA‑AAAGTCTTAA‑GCGGTTGTTTCGTTGTTTTAAAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACgaga                                                                                            <  1:501341/218‑1 (MQ=255)
                                                                                                                          caaaagggatgtggccctggg‑ctAGTGG‑TTGCTGTGAT‑AAGG‑AAGGCGAAGGGGATTGAGATAAAAACCCCGGCGGTAAGCGCC‑AGAT‑AG‑AAATTCTTAA‑GGGGATGTTTCTTTGCTTTATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGAt                                                                                           <  2:327978/213‑1 (MQ=255)
                                                                                                                                   ttGT‑GCCTGTG‑CAAGTGG‑TGGCTTGGAT‑AGAG‑AAGCCGAAGGCGATTGAAAGGAAAACCCCGGCTGTAATCCCC‑ATAT‑AA‑AATGTCTAAA‑GGGGATGTTGCGTTGCTTGATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAg                                                                                 <  2:35485/228‑1 (MQ=255)
                                                                                                                                                        gtgtgtggtaaaaaagaaagagAATGCGATAGAGAGGAACACCCGGGAGTTATTACAC‑AGAA‑AG‑AAAGTGTAAA‑GGGGATGTTTCTTTGCTTTAAAGCCACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGaaa                                                                 <  1:70687/207‑1 (MQ=255)
                                                                                                                                                        cagccagtgaatgag‑aagaCGAATGCGATTGAGATGAAAACACCGGCGCTAAGCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATTTTTCGTGGTTTTATAACCACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGaaa                                                                 <  2:617441/214‑1 (MQ=255)
                                                                                                                                                             gtgAT‑AAAA‑AAGAAGAAGCGGTTTGAGTTAAAAACCCCGGCGTAAATC‑CA‑AGGTAAG‑AAAGTCATAA‑GGGTATGTTTCGTTGCTTTATAGACCCCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGata                                                           <  2:399833/227‑1 (MQ=255)
                                                                                                                                                                          gaCGAATGCGATTGAGATGAAAACACCGGCGGGAATCGCC‑AGAT‑TG‑AAAGTCTTAA‑GCGGATGGTTCGTTGCTTTATAGACACCCGCCTCTTCGG‑CCACCTTGGCCATTTCAGCAGGAAGTAAAAAATCAAAAGGGTTGTCCGCTTTCACCCTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCatattt                                               >  2:570826/1‑226 (MQ=255)
                                                                                                                                                                             gAATGCTATTGAAATAAAACCCCCGCGGGAAAACCCA‑AGAT‑AA‑AAACTCTAAA‑GGTTTTGTTCCGTTGCTTTATAGACGCCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGc                                            <  2:499310/228‑1 (MQ=255)
                                                                                                                                                                               aaaaattttagagaaaaaCCCCGGGGGTAACCCCCAAAAT‑AG‑AAA‑TGTTAAGGAGGGTTTTGCGTTGTTTAACAGCCCCCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGcc                                           <  1:106802/214‑1 (MQ=255)
                                                                                                                                                                                               aaCACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATCGGAAATTGGTATAGATACTATCTCCCCCTGCTTATAGGctgcc                           >  2:106802/1‑223 (MQ=255)
                                                                                                                                                                                                                          aaaatccaaaa‑GGGGATTTTTAGTTGATTTAAAACCACCCGTCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATa  <  2:590052/219‑1 (MQ=255)
                                                                                                                                                                                                                                       |                                                                                                                                                                                                                        
TGCGCCCACTCGCCTTAGCAACAACAATCAACACGGTGGAAGTAAAGAGATCGGCTCCGCAGACAACACAAAGAATCAGCCCCAGAGAGAAGCAAATG‑CCGCCAACCAGTTTTGCCATGCCG‑AAGGGCATTGT‑GCCTGTG‑CCAGTGG‑TTGCTGTGAT‑ATAG‑AAGACGAATGCGATTGAGATGAAAACACCGGCGGTAATCGCC‑AGAT‑AG‑AAAGTCTTAA‑GCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGG‑CCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATA  >  NC_000913/954154‑954589

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