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
A11 F58 I0 R3 223 82.2 2922920 95.2% 2782619 126.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,476,682 G→T 39.6% T22K (ACA→AAA)  U712_17855 ← putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,476,6820GT39.6% 23.8 / 11.6 41T22K (ACA→AAA) U712_17855putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein
Reads supporting (aligned to +/- strand):  ref base G (14/10);  new base T (4/11);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 9.78e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGCCCCGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTG‑AGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAAT  >  CP006881/3476545‑3476819
                                                                                                                                         |                                                                                                                                          
cAGGCCCCGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATg                                                                                                                                            >  7:182900/1‑138 (MQ=255)
  ggCCCCGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTaa                                                                                                                                         <  5:73609/139‑1 (MQ=255)
  ggCCCCGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTGAGATAAAGTa                                                                                                                                          >  7:178992/1‑138 (MQ=255)
    ccccGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTaaaa                                                                                                                                       <  8:230719/139‑1 (MQ=255)
       cGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAACTATCCATTACGCGCGTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGaa                                                                                                                                    <  6:94044/139‑1 (MQ=255)
        ggCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTAAGATAATGTAAAAGAAt                                                                                                                                   >  5:355171/1‑139 (MQ=255)
        ggCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAAACCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACCAGCCGTCTTTTGATATAATTTAAAAGAAt                                                                                                                                   >  4:357565/1‑139 (MQ=255)
        ggCGTCTCCAAACAAAACAAAATTGAAAATACAGCAATCATTTGCAGCGCAAACGCCAAACCAAAGAGCGCAAACAAAATATACAATACGCCCTTTATTGCCAAATAACGAGCCGTCGTTTGAAATAAAATAaaaaaa                                                                                                                                    >  5:199314/1‑138 (MQ=255)
          cGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGt                                                                                                                                 <  8:220036/139‑1 (MQ=255)
              tcCCAACAAATCAAAATTGAAAATACCGCAAACATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTGAGATTATTTAAAAGAatttattt                                                                                                                             >  4:272364/1‑139 (MQ=255)
              tcCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTTCCAAATAACGAGCCGTCGTTTAATAAAATGTAAAAAAATGTAttt                                                                                                                             >  4:135252/1‑139 (MQ=255)
                caaacaaaTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATttg                                                                                                                            <  3:357565/138‑1 (MQ=255)
                       aTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGCTTTGCGATAATGTAAAAGAATGTATttgttggaat                                                                                                                     >  5:224678/1‑134 (MQ=255)
                                 aaaaTACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAAACAAATAACCATTACGCGCTTTATTGCCAAATAACGAGCCGTGATTTCAGAAAATATAAAAGAATGTATTTGTTGAAATG‑AGAATACACg                                                                                                         >  7:121207/1‑139 (MQ=255)
                                      aCCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTAAGATAATGTAAAAGAATGTATTTGTTGAACTG‑AGAATTAAAGACTca                                                                                                    >  1:254820/1‑139 (MQ=255)
                                         ccAATCATTGCCAGCGCAAACCCCAAACAAATCCGCCAAAACCAAATAACAATTACGCGCTTTATTCCCAAATAACGAGCCGTCTTTTAATATAATTAAAAATAATTTTTTTGTTTAACTT‑ATAAAACACGACTCACAt                                                                                                 <  2:95362/138‑1 (MQ=255)
                                                       cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTAAGATAATGTAAAAGAATGTATTTGTTGATCTG‑AGAAATCACGACTCACATTCATGCTTTtctcc                                                                                   >  7:62793/1‑138 (MQ=255)
                                                       cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTGAGATAATTTTAAAGAATTTATTTGTTTTTCAG‑AGATATAACGACTCACATTAATTCGTTTctct                                                                                   >  1:217893/1‑139 (MQ=255)
                                                        gcAATCGCAAATCAAATCAGCCCAAACAAAATATCAATTCCGCGCTTTATTGCAAAATAACGAGCCTTCTTTTAATAAAATTAAAAATAATGTATTTGTTGAACTG‑ATAATCCACGACTCACATTCATGCTTTTCTCTg                                                                                  <  6:355171/139‑1 (MQ=255)
                                                              gcaaatccaatGAGCGAAAACAAAATATACATTACGCTATTTTTCCCAAAAAAACGCGCCTTATTTTAATAAAATTAAAAATATTGTTTTTTTTTAACTG‑ATATTCCACGACTCACATTCATGCTTTTCTCTGcactca                                                                            <  4:111127/136‑1 (MQ=255)
                                                                   tccaatGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGa                                                                                                                                     >  1:33740/1‑78 (MQ=255)
                                                                   tccaatGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGa                                                                                                                                     <  2:33740/78‑1 (MQ=255)
                                                                      aatGAGCGAAAACCAAATATCAATTACGCGATTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAATATTTTTTTTGTTGAACTG‑ATAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacaca                                                                    <  3:182042/139‑1 (MQ=255)
                                                                      aaggaccgcAAACCAAAAAACCATTCCGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCATATAATGTAAAACAATGTATTTGTTGATCTG‑AGAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacaca                                                                    <  3:139888/133‑1 (MQ=255)
                                                                        tGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTGAGATAATGTAAAAGAATGTTTTTGTTGAACAG‑AGAATTCACGACTCACATTAATGCTTTTCTCTTCCCTCACTGacacacc                                                                  >  7:168417/1‑138 (MQ=255)
                                                                                aaCCAAATAACCTTTCCGCGCTTTATTCCAAAAACACTAGCCTTTTTTTCAAAAAATGTAAAATAATTTTTTTGTTCACCTG‑ATAACGCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGa                                                          <  1:52415/139‑1 (MQ=255)
                                                                                 aaaaaaaATCCATTACGCTCTTTATTGCAAAATAACGCGCCTTATTTTAATATAATTTAAAATAATTTATTTGTTTAACTT‑ATAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGAt                                                         <  3:286914/136‑1 (MQ=255)
                                                                                             ttACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTG‑AGAATTAACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATg                                             >  3:34382/1‑139 (MQ=255)
                                                                                             ttACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTTAAAGAATGTTTTTGTTGAACTG‑GGAATTCACGACTCACATTCATGCGTTTCTGTGCACTCACTGACACACACCTCACGATTTTTTTGGGTTg                                             >  5:86950/1‑139 (MQ=255)
                                                                                              gccgcgATTTTTTACCTAATACGGACCAGTTTTTTCAGATATTTTAAAATATTGTTTTTGTT‑TTCTGTATTATTCACGACTCACATTCAAGCTTTTCTCTGCACTCACTGACACCCACCTCACGATTTGTTTGGGATg                                             <  8:121207/136‑1 (MQ=255)
                                                                                                cgcgCTTTATTGCCAAATAACGAGCCGTCTTTTCACATAATTTAAAAAAAATTATTTTTTGAACTG‑AGAATTAAACACTCACAATAATGCTATTATATTCACTAACAGCCAACCAACTCACGATTTTTTTGGGATGTTa                                          >  4:227097/1‑139 (MQ=255)
                                                                                                  cgcTTATTTGCAAAATAACGCGCCGTGTTTTCATAAAATTAAAAAGTATTTTTTTGTTGAACTG‑TCATTTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatg                                        <  1:40037/139‑1 (MQ=255)
                                                                                                  cgatttATTGCAAAAAAACGAGGCGTCTTTTCATTTATTTTAAATGATTGTATTTGTTCAACTT‑CTAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatg                                        <  8:168417/136‑1 (MQ=255)
                                                                                                   gatttATTCCAAAAAACCGCGCGGTCTTTTCATAAAATTAAAAATATTGTATTTGTTCAACTC‑ACAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatga                                       <  2:254820/137‑1 (MQ=255)
                                                                                                        aTTCCCAAATACCGAGCCGTCTTTTCACAAAATGAAAAAGAATGTATTTGTTAAACTG‑AGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGAc                                   <  4:179975/138‑1 (MQ=255)
                                                                                                            ccAAATCACGCGCCGTCTTTTAATAAAAGTAAAAAGAATGTTTTGGTTGACTTG‑CTAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATg                              <  2:91821/139‑1 (MQ=255)
                                                                                                               aaTAACGAGCCGTCTGTTCAGATAATGTAAAAGAATGTATTTGTTGGACTG‑AGAATTCACGACTCACCTTCATGCTTTTCGCTGCACTCACGGACACACACCTCACGAGTTGTTTGGGATGTTATGATGACCGATGccc                           >  6:127518/1‑138 (MQ=255)
                                                                                                                      aGCCGTCGTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTG‑AGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCGCACGATTTGTTTGGGAGGTTATGATGACCGATGCCAGTCAGtt                    >  3:350039/1‑139 (MQ=255)
                                                                                                                           tcgtttGAGATAATGTAAAATAATGTATTTGTTGAACTG‑AGAATTCACGACTCACATTAATGGGTTTCTCTGCACTAACGTCCACACACCGCACGCTTTTTTTGGGTTGTTTTGATGTCCGATGCCAGGCAGTTTat                 >  4:100716/4‑136 (MQ=255)
                                                                                                                              tttCAGATATTTAAATATAATGTATTTGTTGACCTG‑ATATTTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGa             <  3:135252/138‑1 (MQ=255)
                                                                                                                              tttCAGATAATTTAAAATAATGAATTTGTTTAACTT‑ATAATACACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGa             <  8:182900/138‑1 (MQ=255)
                                                                                                                                        tGTAAAAGAATGTATTTGTTGAACTG‑AGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAAt  >  4:180213/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                                          
CAGGCCCCGGCGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTG‑AGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAAT  >  CP006881/3476545‑3476819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A