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 1,069,802 C→G 21.9% A82G (GCG→GGG)  U712_05265 → Putative quinone oxidoreductase YhfP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068811,069,8020CG21.9% 90.0 / 4.1 43A82G (GCG→GGG) U712_05265Putative quinone oxidoreductase YhfP
Reads supporting (aligned to +/- strand):  ref base C (7/26);  new base G (7/3);  total (14/29)
Fisher's exact test for biased strand distribution p-value = 7.21e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTTGCTTATTCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGATGG  >  CP006881/1069667‑1069936
                                                                                                                                       |                                                                                                                                      
aaGTTGCTTATTCCGGCATTAATTACACAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGa                                                                                                                                     <  3:27322/139‑1 (MQ=255)
aaGTTGCTTATTCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGa                                                                                                                                     <  2:27909/139‑1 (MQ=255)
aaGGTGCTTATTCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGa                                                                                                                                     <  8:30857/139‑1 (MQ=255)
  ggtGCTTATTCCTGCATTAATTACACAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAgg                                                                                                                                   <  8:192121/137‑1 (MQ=255)
      cTTATTCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTGTCTTGCAATGATCCGCGTTTTTGGGAgggg                                                                                                                                 >  6:276073/1‑137 (MQ=255)
          ttCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCGCTTCCAATGATAAGCGGTTTTCGGAGGGGGGTGAg                                                                                                                           >  4:97442/1‑139 (MQ=255)
               gCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTGCAATGATACGCGGTTTGGGGAGGGGGGTGAGGTgtt                                                                                                                      >  6:207106/1‑137 (MQ=255)
                  ttaattaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATcgc                                                                                                                   <  4:301053/139‑1 (MQ=255)
                     tttaCAACGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGCGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGAc                                                                                                                <  4:255629/138‑1 (MQ=255)
                     attaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTGTGGTCCAATGATCCGCGGGTTGGGGGGGGGGGGGAGGTGGTGGCGa                                                                                                                 >  1:40720/1‑138 (MQ=255)
                     attaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGa                                                                                                                 <  4:73214/138‑1 (MQ=255)
                     attaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGa                                                                                                                 <  3:97442/138‑1 (MQ=255)
                     attaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGAc                                                                                                                <  3:178995/139‑1 (MQ=255)
                      ttaCAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACa                                                                                                               <  2:30600/139‑1 (MQ=255)
                      ttaCAAAGATGGGCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGAATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGGGATCGCGACa                                                                                                               <  8:192520/139‑1 (MQ=255)
                          aaaGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTCGCGGAGGGGGATGAGGTGATCGCGACAAGCt                                                                                                           <  3:354851/139‑1 (MQ=255)
                                 gTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCGCTTCCAATTATCAGCGTTTTGGGGTGGGGGTTGTGGTGCTAGCGCCAAGCGTTGAGca                                                                                                    >  4:41636/1‑138 (MQ=255)
                                   cTGGCCGTAAATGATGTAGGCAATATCGTCTGAGATTAGCCTATTATTTTAGGCATTGCTGCTGCGGGTCGGGGCGGCTCTTCCAATGATCCGGGTTTTGCGGAGGGGGATGAGTTGATCGCGACAAGCTATGAGCTCg                                                                                                  <  6:299604/139‑1 (MQ=255)
                                      gCCGGAAAAGCAGGAGGCTATATCGTCAGAGAGGATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCgg                                                                                                 <  1:162402/137‑1 (MQ=255)
                                                   gaggCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATgg                                                                                  <  2:288138/139‑1 (MQ=255)
                                                        aaTATCGTCACAGAGTATCCGGTTTTTTTTGGCATTGATGCTGCGGGAACGGGAGTCTCTTCCACTGATCCGAGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGAt                                                                             <  4:8042/139‑1 (MQ=255)
                                                          tatCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTa                                                                           <  8:108320/139‑1 (MQ=255)
                                                            tCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGGCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTaa                                                                          <  5:276073/138‑1 (MQ=255)
                                                                cAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTGTGGTGCCATGATCCCCGGTTTTCGGGGGGGGGGGAGGTGATCGCCCCCAGCTCTGTCCTAGGTGGCTCACGGGATGGCGGGTTTAGTTaa                                                                     >  3:270388/1‑139 (MQ=255)
                                                                        aTCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTGTCTTCCAATGATCCGCGGTTTGCGGAGGGGGATTAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTc                                                             >  2:249648/1‑139 (MQ=255)
                                                                         tCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGGTTTGCGGGGGGGGTGGAGGTGATCGCGACCAGCTTTGAGCGCGGGGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCg                                                            >  8:189400/1‑139 (MQ=255)
                                                                              ttATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGcc                                                       <  4:270388/139‑1 (MQ=255)
                                                                               tATTTTAGGCATTGATGCTGCGGGTACGGTCGTGTCTTACAATGATACCCGTTTTGGGGAGGGGGGTGAGGTGGTGGCGCACACCAATGAGGACGGTTGGTAACCTGATGGCGGAGTTAGTGAATAAGCGTGGGTggcg                                                      >  6:120290/1‑136 (MQ=255)
                                                                               tATTTTAGGCATTGATGCTGCGGGTACGGTCGTGGCGTGCAATGAAACGCGGTTTGGGGGGGGGGGTGTGGGGATCGCGGCAACCTATGAGCTCGGTGGAGCACGTGATGGCGGCTTAAGTGTATACGCGTCGGTGCCt                                                      >  2:133631/1‑139 (MQ=255)
                                                                               tATTTTAGGCATTGATGCTGCGGGTACGGTCGTGGCGGCCAATGATCCGCGTTTTGCGGTGGGGGCTGAGGGGATCGCGACCAGCTATGAGCTCGGGGTGTCACGGGATGGGGGGTTAAGTGAATACGCTTCGGTggcg                                                      >  3:223481/1‑136 (MQ=255)
                                                                                aTTTTAGGCATTGATGCTGCGGGTACGGTCGGCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGcc                                                       <  7:297413/137‑1 (MQ=255)
                                                                                      ggCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGAc                                                <  1:256905/138‑1 (MQ=255)
                                                                                       gCATTGATGCTGCGGGTACGGTCGTGGCTTCCAATGATACGCGTTTTGCGGAGGGGGATGCGGTGGTCGCGACAAGCTATGAGCTCGGTGTCGCACGGGATGGCGGATTTATTGAATACGCTTGGGTGCCTGGTGAatg                                              >  8:301999/1‑139 (MQ=255)
                                                                                           tGATGCTGCGGGTACGGTCGTGGCGTGCCATGTTCCGCGGTTTGGGGGGGGGGGTGAGGTGGTGGGGGCAAGCTATGAGCTCGGTGTGTCCCGTGATGGCGGCTTTAGTGAATAGGCGTCGGGGGCTGGGGActgggtg                                          >  2:256905/1‑139 (MQ=255)
                                                                                                                             ccGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTCTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCGTTTGCCACAGAATCTTTCGTTAAaagaag        >  2:168287/1‑139 (MQ=255)
                                                                                                                               gggTTTTGCGGTGGGGGATGAGGTCAGCGCGACAAGCTATGAGCTCGGTGGCTCACGTGATGGCGGATTAAGTGAATACGGTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCg      <  4:341888/137‑1 (MQ=255)
                                                                                                                                cggtttGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGa     <  2:75104/136‑1 (MQ=255)
                                                                                                                                cggtttGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGGGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGa     <  8:271847/136‑1 (MQ=255)
                                                                                                                                cgTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGGCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGGGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGa     <  5:120290/139‑1 (MQ=255)
                                                                                                                                 ggtttGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGAt    <  5:162604/137‑1 (MQ=255)
                                                                                                                                 gTTTTGGGGAGGGGGATGAGGTGAGCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTATGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGAt    <  3:41636/139‑1 (MQ=255)
                                                                                                                                  ttttGGGGAGGGGGATGCGGTGATCGCGACAAGCTATGAGCTCGGTGGCTCACGTGATGGCTGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGATg   <  1:133631/139‑1 (MQ=255)
                                                                                                                                    ttGGGGAGGGGGATGAGGGGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGATgg  <  3:291/138‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                      
AAGTTGCTTATTCCGGCATTAATTACAAAGATGGTCTGGCCGGAAAAGCAGGAGGCAATATCGTCAGAGAGTATCCGCTTATTTTAGGCATTGATGCTGCGGGTACGGTCGTCTCTTCCAATGATCCGCGTTTTGCGGAGGGGGATGAGGTGATCGCGACAAGCTATGAGCTCGGTGTCTCACGTGATGGCGGATTAAGTGAATACGCTTCGGTGCCTGGTGACTGGCTGGTGCCTTTGCCACAGAATCTTTCGTTAAAAGAAGCGATGG  >  CP006881/1069667‑1069936

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A