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
A17 F104 I0 R1 40 45.6 1767846 90.1% 1592829 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,158,785 C→T 100% P99L (CCC→CTC)  oxyR → DNA‑binding transcriptional dual regulator OxyR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,158,7850CT100.0% 110.3 / ‑6.7 44P99L (CCC→CTC) oxyRDNA‑binding transcriptional dual regulator OxyR
Reads supporting (aligned to +/- strand):  ref base C (1/1);  major base T (25/14);  minor base G (0/3);  total (26/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGC  >  NC_000913/4158646‑4158918
                                                                                                                                           |                                                                                                                                     
cGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTcac                                                                                                                                    >  2:572955/1‑143 (MQ=255)
   aaaGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGACCGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGCCCGCGGCACATTGGCTTGATTCTCACGGt                                                                                                                                 >  1:347693/1‑143 (MQ=255)
    aaGTGTGGTTCACCCAGGCGGGAGCGCCCCTTGTGGATCAGGCGCGGTCCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGtt                                                                                                                                <  1:326109/143‑1 (MQ=255)
         ttgttCACCGAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGAcc                                                                                                                           <  2:699919/143‑1 (MQ=255)
          tgttCACCGAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGGGAGGTGAAAGTCCTTAAAGCGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCg                                                                                                                          <  1:183910/143‑1 (MQ=255)
           gttCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGGGTGAGGGGACAGGCCATAAAGAGGTGGCAAGCCGGCAGCGCGAGACGATGCCCGGACCGCGGCACACTGGTTTGATTACCGCACTTCGGCCGt                                                                                                                         >  2:400123/1‑143 (MQ=255)
            ttCAGCCAGGCGGGAATGCTGCTGGTGGATATGGCTCGTATCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATTTCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTa                                                                                                                        <  2:180450/143‑1 (MQ=255)
            ttCACCCGGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTa                                                                                                                        <  2:659286/143‑1 (MQ=255)
            ttCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTCGGACCGTa                                                                                                                        >  1:728147/1‑143 (MQ=255)
            tccACCCGGGCCGGAATGCTGCTGGCGGGTCAGGCGCGTGCCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTa                                                                                                                        <  2:655681/141‑1 (MQ=255)
             tCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACCGTTGGACCGTAc                                                                                                                       >  1:334630/1‑143 (MQ=255)
                 ccAGGCGGGGATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTTCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGc                                                                                                                   <  2:539471/143‑1 (MQ=255)
                   gggCGGGAATGCTGCCGGTGGATCAGGCGCGTGCCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTa                                                                                                                 <  2:267622/142‑1 (MQ=255)
                   aGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTa                                                                                                                 >  1:423889/1‑143 (MQ=255)
                       gggAATGCTGCTGGTGGATCAGGCGCGTACCGCGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGAGTCTCACAGTTGGACCGTACCTGCGACCGc                                                                                                             >  2:461368/1‑143 (MQ=255)
                           aTGCTGCTGGTGGCTCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCGTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCatat                                                                                                         <  2:506227/143‑1 (MQ=255)
                            tgctgcTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCCACCGCAtatt                                                                                                        >  1:370903/1‑143 (MQ=255)
                            tgctgcTGGTGGAACAGGCGCGTACCGGGCTGCGTGGGGGGAAAGACCTTAAAGAGATGGCAAGGCAGCATGGCGAGACGATGTCCGGACCGCTGCACATTGGCTTGGTTCTCACAGTTGGACCGTACCTGCTACCGCatact                                                                                                        >  2:607972/1‑141 (MQ=255)
                             gctgctGGTGGATCAGGCGCGTACCGTGCTGCGTAAGATGAAAGACATTGATGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGCTTCTCACCGCTGGCCCGTACCTGCTACCGcctccca                                                                                                       >  1:243960/1‑137 (MQ=255)
                               tgctgGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATc                                                                                                     >  1:111521/1‑143 (MQ=255)
                                 ctgGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCCAGCCAGCAGGGCGAGACGATGTACGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCCTATTATccc                                                                                                   >  1:53051/1‑143 (MQ=255)
                                   ggtggATCGTGCGCGTACCGTGCTCGGTGAGGTGAAAGTCCGTACAGAGATCGCAAGCCAGCAGGGCGCGACGATGTCCGGACCGCTGCACATTGCTTTGATTCTCACAGTTGGAACGTACCTGCTACCTCATATTATCCCTa                                                                                                 <  2:608397/143‑1 (MQ=255)
                                    gtggATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTAt                                                                                                >  2:792804/1‑143 (MQ=255)
                                    gtggATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATAGTATCCCTAt                                                                                                >  1:211398/1‑143 (MQ=255)
                                      ggAGCAGGCGCGTGCCGGGCTGCGGGGGGTGAAAGTCCTTAGAGAGCTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTAtgc                                                                                              <  2:164884/143‑1 (MQ=255)
                                       gATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTAtgct                                                                                             >  1:881586/1‑143 (MQ=255)
                                       gATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTAtgct                                                                                             >  1:133282/1‑143 (MQ=255)
                                             gcgcGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGAGGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGCACCTGCTACCGCATAGTATCCCTATGCTGCAcaa                                                                                       >  2:515712/1‑141 (MQ=255)
                                                     cGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACACTGGTTTGTTTCTCACAGTTGGCCCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGCCCtctc                                                                               >  2:819668/1‑143 (MQ=255)
                                                      gTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTcc                                                                              <  1:424346/143‑1 (MQ=255)
                                                                aGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGaa                                                                    >  1:338136/1‑143 (MQ=255)
                                                                       aGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCCTATTATCCCTATGCTGCACCAGACCTTTCCAACGCTGGAAATGTagc                                                             >  1:199060/1‑141 (MQ=255)
                                                                           cTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTATGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCACACCTTTCCAAAGCGGGAAATGTCTCTGCa                                                         >  2:486224/1‑143 (MQ=255)
                                                                                agagATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTACCAAAGCTGGGAGCGTATCTGCATGAAg                                                    >  2:448076/1‑143 (MQ=255)
                                                                                       gCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCGTGAAGCACGGAc                                             >  1:475181/1‑143 (MQ=255)
                                                                                       gCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACAGTGGTTTGATTCTCACAGTTGGAACGTACCTGCTACCGCAGATTATCCCTATGCTGCACGAGACCTTTACAACGCTGGAAGGGTATCTGCGTGAAGCACAGAc                                             >  2:252139/1‑143 (MQ=255)
                                                                                         aaGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACAGCATATTATCCCTATGCTGCACCTGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGAccc                                           >  1:164140/1‑143 (MQ=255)
                                                                                                    gCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTg                                <  2:206966/143‑1 (MQ=255)
                                                                                                      gctgcGATCTCGGCACCGCTGCTCTTTGGTTTGATTCTCACCGTTGGACCGTCCCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGgc                              <  2:682292/139‑1 (MQ=255)
                                                                                                      gagaCGCTGTCCGGCCCGCTGCACATTGGTTTGTTTCTCACAGATGGATCGGACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGgc                              <  1:448568/143‑1 (MQ=255)
                                                                                                               tacGGCCCGCCGCACATTGGGTTGACTCGCACCGGTGGACCGTGCCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGa                     <  2:587088/141‑1 (MQ=255)
                                                                                                                         tGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAACCACAGACCCACCAGTTACTGGCGCCACTGGCCCGCGGCaac           >  2:360168/1‑142 (MQ=255)
                                                                                                                                tGGTTTGATTCGCACAGTGTGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGAtt    <  2:334630/143‑1 (MQ=255)
                                                                                                                                  gTTTGATTCGCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGc  <  1:572955/143‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                     
CGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGC  >  NC_000913/4158646‑4158918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A