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
A12 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,987,655 Δ1 bp coding (120/633 nt) yqeH → putative LuxR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,987,6540G.96.4% 239.6 / 2.8 55coding (119/633 nt)yqeHputative LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base . (25/28);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 4.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

AAAGTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGTGGCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCGATT  >  NC_000913/2987558‑2987749
                                                                                                |                                                                                               
aaaGTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTAtgtgccc                                                                                              >  1:322576/1‑97 (MQ=255)
aaaGTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGTGccc                                                                                              <  1:1120635/100‑1 (MQ=255)
 atgTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATACCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTAtgtgcccg                                                                                             >  1:882499/3‑96 (MQ=255)
  aGTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGTGcccg                                                                                             <  1:433460/99‑2 (MQ=255)
     cTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCgaaga                                                                                        >  1:50587/1‑100 (MQ=255)
     cTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCgaaga                                                                                        >  2:305042/1‑100 (MQ=255)
        aCATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAg                                                                                     <  1:25315/100‑1 (MQ=255)
          aTGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGtt                                                                                   >  2:669156/1‑100 (MQ=255)
           tGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTc                                                                                  >  1:137891/1‑100 (MQ=255)
           tGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTc                                                                                  <  1:963468/100‑1 (MQ=255)
           tGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTc                                                                                  >  1:798182/1‑100 (MQ=255)
           tGCAATAGTTGCTAAATGCATTGCCAAATAATGCCAGACGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGtt                                                                                   >  2:804171/1‑99 (MQ=255)
            gCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCACACTAGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCa                                                                                 >  2:314416/1‑100 (MQ=255)
            gCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTc                                                                                  >  2:264823/1‑99 (MQ=255)
            gCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCa                                                                                 <  2:274377/100‑1 (MQ=255)
             cAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCat                                                                                >  1:768525/1‑100 (MQ=255)
              aaTAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCata                                                                               <  1:527610/100‑1 (MQ=255)
                  gTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATAtttt                                                                           <  1:472687/100‑1 (MQ=255)
                   ttGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTa                                                                          <  1:1207121/100‑1 (MQ=255)
                      cTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATc                                                                       >  1:147717/1‑100 (MQ=255)
                        cAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgt                                                                     >  2:1011238/1‑100 (MQ=255)
                          aTGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtgg                                                                   <  2:57448/100‑1 (MQ=255)
                          aTGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtgg                                                                   <  2:1176100/100‑1 (MQ=255)
                            gCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtggtg                                                                 <  2:399173/100‑1 (MQ=255)
                             cATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtggtgt                                                                >  2:1118759/1‑100 (MQ=255)
                              aTTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtggtgtg                                                               <  1:233104/100‑1 (MQ=255)
                                tGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCgtggtgtggt                                                             <  1:381276/100‑1 (MQ=255)
                                 gCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTa                                                            >  2:424890/1‑100 (MQ=255)
                                     aataatGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAg                                                        <  1:2075/100‑1 (MQ=255)
                                       taatGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGt                                                      >  1:819571/1‑100 (MQ=255)
                                           gCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCt                                                  >  2:862958/1‑100 (MQ=255)
                                            ccAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCtt                                                 >  1:1007911/1‑100 (MQ=255)
                                               gaagaGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAAc                                              <  2:681951/100‑1 (MQ=255)
                                               gaagaGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAAc                                              <  2:440344/100‑1 (MQ=255)
                                                aagaGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACa                                             <  2:13116/100‑1 (MQ=255)
                                                aagaGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACa                                             <  1:424894/100‑1 (MQ=255)
                                                    gTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACaaaaa                                         <  1:987984/100‑1 (MQ=255)
                                                     tCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACaaaaaa                                        <  1:1011247/100‑1 (MQ=255)
                                                      cACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAAc                                       <  2:658193/100‑1 (MQ=255)
                                                        ccGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACca                                     >  1:600919/1‑100 (MQ=255)
                                                         cgcgTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACcac                                    <  1:1046517/100‑1 (MQ=255)
                                                          gcgTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACcaca                                   >  2:579292/1‑100 (MQ=255)
                                                                 cAGTATTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCgag                            <  1:745370/100‑1 (MQ=255)
                                                                     aTTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACACAACACCACAATGCGAGATTa                        >  2:1082950/1‑100 (MQ=255)
                                                                     aTTGCGCAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTa                        >  2:361133/1‑100 (MQ=255)
                                                                        gcgcAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGc                     >  1:329496/1‑100 (MQ=255)
                                                                        gcgcAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGc                     >  2:749464/1‑100 (MQ=255)
                                                                         cgcAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTAAATTAAAAAAAAACCACAATGCGAGATTAAGCg                    <  2:824366/100‑1 (MQ=255)
                                                                          gcAAACTCGTGTTTTTGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCgg                   <  2:137889/100‑1 (MQ=255)
                                                                                     tttttGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTg        <  1:514073/100‑1 (MQ=255)
                                                                                     tttttGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTg        <  2:125654/100‑1 (MQ=255)
                                                                                       tttGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTc      <  1:359349/100‑1 (MQ=255)
                                                                                       tttGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTc      <  1:932368/100‑1 (MQ=255)
                                                                                        ttGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCg     <  2:742572/100‑1 (MQ=255)
                                                                                         tGTATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCGa    >  2:729651/1‑100 (MQ=255)
                                                                                           tATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCGAtt  >  2:200781/1‑100 (MQ=255)
                                                                                           tATGT‑GCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCGAtt  >  2:891303/1‑100 (MQ=255)
                                                                                                |                                                                                               
AAAGTCTTACATGCAATAGTTGCTCAATGCATTGCCAAATAATGCCAGAAGAGTCACCGCGTTTGCAGTATTGCGCAAACTCGTGTTTTTGTATGTGGCCCGAAGAAAGTTCATATTTTAATCGTGGTGTGGTAGAAGGTATCTTAACAAAAAACCACAATGCGAGATTAAGCGGATATATTTTTGTCGATT  >  NC_000913/2987558‑2987749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A