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
A10 F1 I2 R1 757 38.1 1607544 96.5% 1551279 117.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,474,138 (A)6→7 coding (15/594 nt) bdcR → transcriptional repressor for divergent bdcA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,474,1321.A97.6% 127.4 / ‑3.4 41coding (9/594 nt)bdcRtranscriptional repressor for divergent bdcA
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base A (20/20);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

CACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473996‑4474261
                                                                                                                                         |                                                                                                                                  
cACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aa                                                                                                                                  >  1:230590/1‑139 (MQ=255)
  ccGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaa                                                                                                                                >  2:85704/1‑139 (MQ=255)
           cGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAAtct                                                                                                                       <  2:511629/139‑1 (MQ=255)
                 ccACCGAGGATGAGAACTTTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACCAAACTATTTTAACTTTCTGTCAACAGGTCTTGGAATGGTCACTAAAAA‑AACAATCTCGCGtt                                                                                                                 >  2:208989/1‑139 (MQ=255)
                 ccACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAAtctc                                                                                                                      <  1:573819/134‑1 (MQ=255)
                 ccACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAAtctc                                                                                                                      >  2:573819/1‑134 (MQ=255)
                       aGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGgt                                                                                                           >  1:144480/1‑139 (MQ=255)
                       aGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGgt                                                                                                           <  1:598352/139‑1 (MQ=255)
                       aGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGgt                                                                                                           >  2:743727/1‑139 (MQ=255)
                                         ccTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCt                                                                                         <  1:743727/139‑1 (MQ=255)
                                              aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGGCGTTTCGCTCCTGa                                                                                    <  2:493428/139‑1 (MQ=255)
                                              aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGa                                                                                    >  1:770778/1‑139 (MQ=255)
                                               aaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                   <  2:358260/139‑1 (MQ=255)
                                                aaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGc                                                                                  <  1:85704/139‑1 (MQ=255)
                                                   cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTcg                                                                                                                     <  2:652852/101‑1 (MQ=255)
                                                   cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTcg                                                                                                                     >  1:652852/1‑101 (MQ=255)
                                                    gcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTACTGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGc                                                                              >  2:580249/1‑139 (MQ=255)
                                                                  cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                >  2:410673/1‑139 (MQ=255)
                                                                    tGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaaa                                                              >  2:264817/1‑139 (MQ=255)
                                                                            tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCtttt                                                      >  2:110126/1‑139 (MQ=255)
                                                                                   cATGCATTACATAACTGTTTTAACTTTCTGTCAACAGGTCTTGTAATGGTCACTAAAAA‑AACAATCACGCGTTCCAGGTCGTCACAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaa                                               >  1:167857/1‑139 (MQ=255)
                                                                                    aTGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaa                                              <  2:770778/139‑1 (MQ=255)
                                                                                     tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                             >  2:179200/1‑139 (MQ=255)
                                                                                     tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCCCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAAGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                             >  2:381331/1‑139 (MQ=255)
                                                                                        aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCa                                                                 >  2:96847/1‑116 (MQ=255)
                                                                                        aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCa                                                                 <  1:96847/116‑1 (MQ=255)
                                                                                            cAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaa‑aaa                                                                                                                            >  2:287419/1‑51 (MQ=255)
                                                                                            cAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaa‑aaa                                                                                                                            <  1:287419/52‑2 (MQ=255)
                                                                                             aaaaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCg                                     <  2:144480/139‑1 (MQ=255)
                                                                                                 cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAATAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGc                                 >  1:567479/1‑139 (MQ=255)
                                                                                                    ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCg                                     >  2:778038/1‑132 (MQ=255)
                                                                                                    ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCg                                     <  1:778038/132‑1 (MQ=255)
                                                                                                    ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                              <  2:567479/139‑1 (MQ=255)
                                                                                                    ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                              >  1:51596/1‑139 (MQ=255)
                                                                                                       tAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                           <  2:324995/139‑1 (MQ=255)
                                                                                                       tAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                           <  1:264817/139‑1 (MQ=255)
                                                                                                         aCTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAgtg                         <  1:179200/139‑1 (MQ=255)
                                                                                                           tttCTGTCAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGtt                       <  1:110126/139‑1 (MQ=255)
                                                                                                                  cAACAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAg                <  1:580249/139‑1 (MQ=255)
                                                                                                                   aaCAGGTTTTGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               <  1:410673/139‑1 (MQ=255)
                                                                                                                           ttGTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAtt       >  2:176383/1‑139 (MQ=255)
                                                                                                                             gTAATGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTAt     >  2:24143/1‑139 (MQ=255)
                                                                                                                                aTGGTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCtt  >  2:744911/1‑139 (MQ=255)
                                                                                                                                   gTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                           >  1:235480/1‑111 (MQ=255)
                                                                                                                                   gTCACTAAAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                           <  2:235480/111‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                  
CACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAA‑AACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473996‑4474261

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A