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
A1 F112 I0 R1 62 38.0 1654010 89.9% 1486954 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 639,694 G→T 21.1% intergenic (+186/‑59) ahpC → / → ahpF alkyl hydroperoxide reductase, AhpC component/alkyl hydroperoxide reductase, AhpF component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913639,6940GT21.1% 76.7 / 13.7 47intergenic (+186/‑59)ahpC/ahpFalkyl hydroperoxide reductase, AhpC component/alkyl hydroperoxide reductase, AhpF component
Reads supporting (aligned to +/- strand):  ref base G (21/15);  new base T (6/4);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

CACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAATTGACCAAGCCTGTTGAG  >  NC_000913/639554‑639818
                                                                                                                                            |                                                                                                                             
cACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCa                                                                                                                             <  1:250379/143‑1 (MQ=255)
    ccGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGACATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCa                                                                                                                         >  1:189082/1‑143 (MQ=255)
          acttacttGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCAAATTTTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGc                                                                                                                   >  1:643089/1‑143 (MQ=255)
            ttacttGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCg                                                                                                                 >  1:247282/1‑143 (MQ=255)
            ttacttGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTCTCTTCCCCGCCCCATTATGCCGGCTTCGTCCTGGTAGCCg                                                                                                                 >  1:257/1‑143 (MQ=255)
               cttGTGTAACCTCTCGTGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCag                                                                                                              <  2:659940/143‑1 (MQ=255)
                ttGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCaga                                                                                                             <  1:805362/143‑1 (MQ=255)
                ttGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCaga                                                                                                             <  1:569069/143‑1 (MQ=255)
                  gtgtCAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAgg                                                                                                           <  2:274658/143‑1 (MQ=255)
                  gtgtAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAgg                                                                                                           >  1:92480/1‑143 (MQ=255)
                         cTCCCGGGGATTCACAGGCTAGCCGCCTTGCCCTGATGTGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCCGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTg                                                                                                    <  1:640213/143‑1 (MQ=255)
                                  aTTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTGATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCAGAGGCCGCTTGCatgatgat                                                                                           <  1:350084/143‑1 (MQ=255)
                                      acaGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCAGGATGATGttt                                                                                       >  2:633063/1‑143 (MQ=255)
                                         ggCTAGCCGCCTTGCTCTGACGCGACATACTCCGGTAATTTACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTaaa                                                                                    <  1:221022/143‑1 (MQ=255)
                                          gCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTTTTCGTGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCCTGATGATGTTTAAAg                                                                                   >  1:156103/1‑143 (MQ=255)
                                          gCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTCCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAg                                                                                   >  2:628450/1‑143 (MQ=255)
                                             aGCCGGCGTGGTCTGACGCGAAAGACCTCGGAAATTCACCTAAGTCTCCGGGTGCTGCGGCACCCGATTTTCTACCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGccc                                                                                <  1:239547/143‑1 (MQ=255)
                                                 gccTGGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACACGATTTTCTTCCCCGCACCACGATGCCAGCTTCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGga                                                                            <  1:587222/143‑1 (MQ=255)
                                                 gccGTGCTCTGACGCGACATACTGCGGAAATTCACCTTATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGga                                                                            <  2:269927/143‑1 (MQ=255)
                                                       ctctGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTACAGCCCAGGAGATaaa                                                                      >  2:205490/1‑143 (MQ=255)
                                                          tGACGCGAAATACTTCGGAAATTCACCTAATTTTGCGGGTTCGTGGGCGCCGGAGTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACAt                                                                   >  1:194545/1‑143 (MQ=255)
                                                          tGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACac                                                                   >  2:71018/1‑142 (MQ=255)
                                                                         cGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAatat                                                    >  2:686777/1‑143 (MQ=255)
                                                                          ggAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCACGCACCATGATGCAAGCTTGATCCAGGTAGCCGCAGAGGCCGCCTGCATGATGATGTTTAAAGCACAGCAGATAAACATGCCCCCCAAAAATATg                                                   >  2:760254/1‑143 (MQ=255)
                                                                           gAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGa                                                  <  1:292074/143‑1 (MQ=255)
                                                                              aTTCACCTAATTCGTCGGGGGCTGAGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGaaaa                                               <  2:49047/143‑1 (MQ=255)
                                                                                 cACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAaactc                                            >  1:22008/1‑143 (MQ=255)
                                                                                   ccTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGCTAAACATGCTCGACCCAAATATGAAaactcaa                                          >  1:143004/1‑143 (MQ=255)
                                                                                    cTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCACAGGAGATAAACATGCTCGACACAAGTATGAAaacacaac                                         >  1:488354/1‑143 (MQ=255)
                                                                                     tAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAaactcaac‑t                                       >  1:403502/1‑143 (MQ=255)
                                                                                      aaTTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCAGCGGCCGCTTGCATGATGATGTTCACAGCCCAGGAGACAAACATGCCCGACACAACTATGACaactaagc‑tc                                      >  2:736473/1‑143 (MQ=255)
                                                                                      aaTTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAACTAAGCAaacacaacgc                                       >  2:210919/1‑141 (MQ=255)
                                                                                        ttcgtcGGGTGCTGCGGCACCCGATCTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAActcaac‑tcaa                                    <  2:227787/143‑1 (MQ=255)
                                                                                          aatcGGGTGCCGCAGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAgg                                  >  1:435356/3‑143 (MQ=255)
                                                                                               ggTGCCGCAGCACCCGATTTTCTTCCCCGCACTATGATGCGAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGAGGATGTTTAAAGCCGAGGAGATAGACATGCTCGACACAAATATGAAAACTAAGC‑TCAAGGCTGAc                             >  2:428513/1‑143 (MQ=255)
                                                                                               ggTGCCGCAGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCGTGCATGATGATGATTAAAGCCCAGGAGATAAACATGCTCGACACACATATGAAAACTCAAC‑TCAAGGCTTAc                             >  2:403880/1‑143 (MQ=255)
                                                                                                     gcGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTCGCCGCAAAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTgag                       >  1:692494/1‑143 (MQ=255)
                                                                                                      cGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATAGAAACTCAAC‑TCAAGGCTTACCTGgaga                      >  1:110346/1‑143 (MQ=255)
                                                                                                          aCCCGATGTTCTTCCCCGCACCATGAGGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAAtt                  <  2:71409/143‑1 (MQ=255)
                                                                                                            ccGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCATC‑TCAAGGCTTACCTTGAGAAATTGa                <  1:398987/143‑1 (MQ=255)
                                                                                                            ccGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAATTGa                <  2:643089/143‑1 (MQ=255)
                                                                                                             cGATTTTCTTCCCCGCACCATGATGCAAGCTTCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAATTGAc               >  1:821600/1‑143 (MQ=255)
                                                                                                             cGATTTTCTTCCCCGCACCATGATACAGGCTGCACCGAGGTAGCCGCAGAGGCCGCTCGCCTGATGATGTATAAAGACCACGAGATAAACATGCCCCAGAGACATATGACAA‑ACAACATCAAGTCTTACCTTGACAAACTGAc               >  2:737291/1‑143 (MQ=255)
                                                                                                                       ccccGCCCCCGGATGCAAGCTGCATCCAGGTGGCCGCAGAGGGCGCTTGCATGATGATGTTTAACGCCCGGGAGCGAAATCCGATCGACACAGATTTTAAGGCTCAAC‑TCAAGGCTTACCTTGAGAAATTGACCAAGCCTGtt     <  2:804229/143‑1 (MQ=255)
                                                                                                                         ccGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAATTGACCAAGCCTGTTGa   <  2:660929/143‑1 (MQ=255)
                                                                                                                         ccGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTAGACACGAATTATTAATCGCAAC‑TCAAGGCTTACCTTGAGAAATTGACCAAGCCTGTTGa   >  1:599112/1‑143 (MQ=255)
                                                                                                                          cGCACCATGAGGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGCTTAAAGCCCAGGAGATAAACATGCGCGACACAAATATGAAAACTCAAC‑TCACGGCCTACCTCGCGAAATGGACCAAGCCGGCTGAg  >  2:768998/1‑143 (MQ=255)
                                                                                                                                            |                                                                                                                             
CACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATTCACCTAATTCTTCGGGTGCTGCGGCACCCGATTTTCTTCCCCGCACCATGATGCAAGCTGCATCCAGGTAGCCGCAGAGGCCGCTTGCATGATGATGTTTAAAGCCCAGGAGATAAACATGCTCGACACAAATATGAAAACTCAAC‑TCAAGGCTTACCTTGAGAAATTGACCAAGCCTGTTGAG  >  NC_000913/639554‑639818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A