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 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

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.A98.0% 158.1 / ‑3.7 50coding (9/594 nt)bdcRtranscriptional repressor for divergent bdcA
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base A (27/22);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑T‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCT  >  NC_000913/4474018‑4474260
                                                                                                                    |                                                                                                                                
gAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAgg                                                                                                           <  1:870937/139‑1 (MQ=255)
 aGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgt                                                                                                          <  1:859913/139‑1 (MQ=255)
     tGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgtcgtc                                                                                                      >  2:831580/1‑139 (MQ=255)
             gTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgtcgtc                                                                                                      >  2:703054/1‑131 (MQ=255)
             gTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgtcgtc                                                                                                      <  1:703054/131‑1 (MQ=255)
              tCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGtt                                                                                             >  1:673251/1‑139 (MQ=255)
               cTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                            <  1:585555/139‑1 (MQ=255)
                  aCCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGc                                                                                         >  1:409958/1‑139 (MQ=255)
                        aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGa                                                                                   >  1:279064/1‑139 (MQ=255)
                         aaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAAGTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                  <  2:673251/139‑1 (MQ=255)
                             cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgt                                                                                                          <  2:643187/111‑1 (MQ=255)
                             cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGgt                                                                                                          >  1:643187/1‑111 (MQ=255)
                             cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAgg                                                                              >  1:978875/1‑139 (MQ=255)
                                          tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                  <  1:925095/122‑1 (MQ=255)
                                          tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                  >  2:925095/1‑122 (MQ=255)
                                          tCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGACGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGc                                                                 >  2:667006/1‑139 (MQ=255)
                                                               tGCATTTCAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                            <  1:38776/91‑1 (MQ=255)
                                                               tGCATTTCAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                            >  2:38776/1‑91 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACAA‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCATGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                            >  2:498411/1‑139 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                  <  2:751647/101‑1 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                  >  1:751647/1‑101 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                            >  2:114344/1‑139 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                            >  1:508161/1‑139 (MQ=255)
                                                               tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                            >  2:848235/1‑139 (MQ=255)
                                                                gCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaaa                                           >  1:868736/1‑139 (MQ=255)
                                                                  aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCa                                                                                                   >  2:792576/1‑81 (MQ=255)
                                                                  aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCa                                                                                                   <  1:792576/81‑1 (MQ=255)
                                                                  aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                         >  1:492104/1‑139 (MQ=255)
                                                                  aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                         >  1:361714/1‑139 (MQ=255)
                                                                  aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                         >  2:406512/1‑139 (MQ=255)
                                                                    tACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGtt                                       >  1:855125/1‑139 (MQ=255)
                                                                        aaaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGa                                   <  1:831580/139‑1 (MQ=255)
                                                                         aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGt                                                           <  1:564196/114‑1 (MQ=255)
                                                                         aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGt                                                           >  2:564196/1‑114 (MQ=255)
                                                                           cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAcc                                                <  1:258553/123‑1 (MQ=255)
                                                                           cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAcc                                                >  2:258553/1‑123 (MQ=255)
                                                                              ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                 <  1:899328/71‑1 (MQ=255)
                                                                              ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                 >  2:899328/1‑71 (MQ=255)
                                                                              ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                            >  2:165488/1‑76 (MQ=255)
                                                                              ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                            <  1:165488/76‑1 (MQ=255)
                                                                              ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                             >  2:1099376/1‑139 (MQ=255)
                                                                                ttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaa                                                              <  2:829109/104‑1 (MQ=255)
                                                                                ttAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaa                                                              >  1:829109/1‑104 (MQ=255)
                                                                                   aCTTTCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAgtg                        <  2:868736/139‑1 (MQ=255)
                                                                                     tttCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                             >  2:480934/1‑132 (MQ=255)
                                                                                     tttCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                             <  1:480934/132‑1 (MQ=255)
                                                                                       tCTGTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGc                    <  2:492104/139‑1 (MQ=255)
                                                                                          gTCAACAGGTTTTGTAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGa                 <  2:279064/139‑1 (MQ=255)
                                                                                                        tAATGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATc   <  1:848235/139‑1 (MQ=255)
                                                                                                         aaTGGTCAC‑TAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCt  <  2:978875/139‑1 (MQ=255)
                                                                                                                    |                                                                                                                                
GAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCAC‑T‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCT  >  NC_000913/4474018‑4474260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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