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
A23 F66 I1 R1 33 61.7 2789148 95.4% 2660847 127.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA BS168_reference_genome 1,693,526 (A)7→8 coding (1031/1611 nt) fliF → flagellar basal‑body M‑ring protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*BS168_reference_genome1,693,5191.A96.3% 185.5 / ‑0.4 54coding (1024/1611 nt)fliFflagellar basal‑body M‑ring protein
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base A (27/25);  total (28/26)
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

TTGCAGTCAGCGCTGAAAAGGTATCTGAAACATATCAGGGCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACG‑AAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTGATGCCAAAAACACTGCG  >  BS168_reference_genome/1693385‑1693647
                                                                                                                                        |                                                                                                                                 
ttGCAGTCAGCGCTGAAAAGGTATCTGAAACATATCAGGGCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACG‑aaa                                                                                                                                >  4:263385/1‑138 (MQ=255)
      tCAGCGCTGAAAAGGTATCTGAAACATATCAGGGCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACG‑aaaaaaaa                                                                                                                           >  7:88262/1‑136 (MQ=255)
                                  tCAGGGCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCg                                                                                             <  5:233860/139‑1 (MQ=255)
                                      ggCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAAtt                                                                                         >  7:96724/1‑139 (MQ=255)
                                      ggCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAAtt                                                                                         >  7:54253/1‑139 (MQ=255)
                                      ggCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAAtt                                                                                         >  1:336301/1‑139 (MQ=255)
                                      ggCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAAtt                                                                                         >  7:206128/1‑139 (MQ=255)
                                         gACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCa                                                                                       >  8:97823/1‑138 (MQ=255)
                                          aCGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCAt                                                                                      >  3:220052/1‑138 (MQ=255)
                                          aCGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCAt                                                                                      >  5:319925/1‑138 (MQ=255)
                                           cGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATa                                                                                     >  6:338520/1‑138 (MQ=255)
                                           cGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGATAACCGAATTCATa                                                                                     >  7:311953/1‑138 (MQ=255)
                                                 aGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAAt                                                                              <  3:242717/139‑1 (MQ=255)
                                                       cggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTg                                                                         >  2:270956/1‑138 (MQ=255)
                                                       cggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        <  5:339635/139‑1 (MQ=255)
                                                       cggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        <  1:174116/139‑1 (MQ=255)
                                                       cggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        <  4:220052/139‑1 (MQ=255)
                                                        ggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        >  6:339635/1‑138 (MQ=255)
                                                        ggcggAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        >  8:51177/1‑138 (MQ=255)
                                                            gAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTc                                                                   >  6:115809/1‑139 (MQ=255)
                                                             aaCTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTcc                                                                  >  1:142631/1‑139 (MQ=255)
                                                                 gCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTtat                                                              <  6:29250/139‑1 (MQ=255)
                                                                  ccGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTtat                                                              <  7:322617/138‑1 (MQ=255)
                                                                   cGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTtat                                                              >  2:33068/1‑137 (MQ=255)
                                                                        ccGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCa                                                       <  2:142631/139‑1 (MQ=255)
                                                                        ccGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCa                                                       <  5:338520/139‑1 (MQ=255)
                                                                        ccGGCGAGGAAGATGTTACAAATTATAAGGCGGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGGTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCa                                                       <  6:157550/139‑1 (MQ=255)
                                                                                     tGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAt                                          <  3:263385/139‑1 (MQ=255)
                                                                                     tGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAt                                          <  8:88262/139‑1 (MQ=255)
                                                                                       ttACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAtt                                         <  7:97823/138‑1 (MQ=255)
                                                                                       ttACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAtt                                         <  7:70026/138‑1 (MQ=255)
                                                                                         taaaaTTATAACGCCGACGGGGAAAATACCGAAACCGGGAAATAACT‑AAAAAAA‑CACCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCa                                       <  5:291761/136‑1 (MQ=255)
                                                                                         aCAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCa                                       <  8:206128/138‑1 (MQ=255)
                                                                                          cAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAg                                     <  1:270956/139‑1 (MQ=255)
                                                                                           aaaTTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGt                                    <  8:54253/139‑1 (MQ=255)
                                                                                             aTTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTaa                                  >  5:321703/1‑139 (MQ=255)
                                                                                             aTTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTaa                                  >  1:283943/1‑139 (MQ=255)
                                                                                                ataAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATgg                               >  7:1276/1‑139 (MQ=255)
                                                                                                 taAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATgg                               >  4:227597/1‑138 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGATCT‑ACG‑AAAAAAACCATCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGGCATTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAgccgc                      >  7:317631/1‑139 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        <  6:208415/89‑1 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGa                                                                        >  5:208415/1‑89 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCa                                                       <  6:256610/106‑1 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCa                                                       >  5:256610/1‑106 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAt                                          <  6:303403/119‑1 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGAt                                          >  5:303403/1‑119 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAgccgc                      >  7:134183/1‑139 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAgccgc                      >  1:8395/1‑139 (MQ=255)
                                                                                                         aCGGTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAAGTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAgccgc                      >  3:114580/1‑139 (MQ=255)
                                                                                                            gTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTg                   <  7:51177/139‑1 (MQ=255)
                                                                                                            gTGAAAATACCGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTg                   <  4:139693/139‑1 (MQ=255)
                                                                                                                     ccGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTGATGCCaaa           <  1:33068/138‑1 (MQ=255)
                                                                                                                     ccGAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTGATGCCaaa           >  4:143529/1‑138 (MQ=255)
                                                                                                                       gAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTtata                                                             <  3:69190/86‑1 (MQ=255)
                                                                                                                       gAAAGCGGGAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTtata                                                             >  4:69190/1‑86 (MQ=255)
                                                                                                                               gAACT‑ACGAAAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAAACGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTGATGCCAAAAACACTGCg  <  4:267612/137‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                 
TTGCAGTCAGCGCTGAAAAGGTATCTGAAACATATCAGGGCGACGGTGCAGCCAACGGCGGAACTGCCGGAACCGGCGAGGAAGATGTTACAAATTATAAGGCTGACGGTGAAAATACCGAAAGCGGGAACT‑ACG‑AAAAAAA‑CAGCAACAAAATCAATTACGAGGTTAACCGAATTCATAAAGAAATCGCTGAAAGTCCTTATAAGGTCAGAGATTTAGGGATTCAAGTAATGGTAGAGCCGCCTGATGCCAAAAACACTGCG  >  BS168_reference_genome/1693385‑1693647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A