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
A7 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,013,640 T→C S138P (TCT→CCT)  fliF → flagellar basal‑body MS‑ring and collar protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,013,6400TC100.0% 190.0 / NA 52S138P (TCT→CCT) fliFflagellar basal‑body MS‑ring and collar protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/27);  total (25/27)

TGCGTCTGCGCCTGGCACAACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTTCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTAAATCTGTTACCCGGCCGCGC  >  NC_000913/2013506‑2013773
                                                                                                                                      |                                                                                                                                     
tGCGTCTGCGCCTGGCACAACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCg                                                                                                                                   >  2:1358250/1‑139 (MQ=255)
        cgcCTGGCACAACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCg                                                                                                                           >  2:1300497/1‑139 (MQ=255)
          ccTGGCACAACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGaa                                                                                                                         >  1:1426953/1‑139 (MQ=255)
               cacaACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTAt                                                                                                                    <  1:1201934/139‑1 (MQ=255)
                    caaGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCgg                                                                                                                 >  1:1077233/1‑137 (MQ=255)
                    caaGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCgg                                                                                                                 <  2:1077233/137‑1 (MQ=255)
                                 aaGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGgc                                                                                                  <  2:812298/139‑1 (MQ=255)
                                     cggcgCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGgcgcgc                                                                                              <  2:1426953/139‑1 (MQ=255)
                                     cggcgCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGgcgcgc                                                                                              <  1:844286/139‑1 (MQ=255)
                                      ggcgCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGcgcgcg                                                                                             <  1:1358250/139‑1 (MQ=255)
                                      ggcgCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGcgcgcg                                                                                             <  2:760141/139‑1 (MQ=255)
                                       gcgcGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGt                                                                                            <  1:694798/139‑1 (MQ=255)
                                          cggtcggtTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACa                                                                                         <  2:503534/139‑1 (MQ=255)
                                             tcggtTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCt                                                                                      >  2:1377554/1‑139 (MQ=255)
                                                          gCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGaaa                                                                         <  1:568035/139‑1 (MQ=255)
                                                           cgtGATCAGGAAAAGATTGGTATCAGTCAGTTCAGCGGGCAGGTTGATTATCAGCGGGCGCTGGAAGGCGGGCGTCCTCGTACCATCGAAACCATCTGCCCGGTTAAAAGGGCGCGCGTACATCTGCCAATGCCGAAAc                                                                        >  2:349196/3‑139 (MQ=255)
                                                           cTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTAt                                                                                                                    <  2:741643/95‑1 (MQ=255)
                                                           cTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTAt                                                                                                                    >  1:741643/1‑95 (MQ=255)
                                                              gATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGt                                                                     <  1:248955/139‑1 (MQ=255)
                                                                     aaaaGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTAtt                                                              >  1:60405/1‑139 (MQ=255)
                                                                          tttGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTcc                                                         <  2:858291/139‑1 (MQ=255)
                                                                              gTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGt                                                                                            <  2:202638/100‑1 (MQ=255)
                                                                              gTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGt                                                                                            >  1:202638/1‑100 (MQ=255)
                                                                                 tCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGaaa                                                                         >  1:191114/1‑116 (MQ=255)
                                                                                 tCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGaaa                                                                         <  2:191114/116‑1 (MQ=255)
                                                                                    gCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACaaaa                                               >  2:1433795/1‑139 (MQ=255)
                                                                                       aGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATc                                            <  1:450529/139‑1 (MQ=255)
                                                                                         ttCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAgggg                                                                                                   <  2:326064/82‑1 (MQ=255)
                                                                                         ttCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAgggg                                                                                                   >  1:326064/1‑82 (MQ=255)
                                                                                         ttCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATccc                                          >  1:1048298/1‑139 (MQ=255)
                                                                                            aGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCtt                                       <  2:636935/139‑1 (MQ=255)
                                                                                              cGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCt                                     >  2:593687/1‑139 (MQ=255)
                                                                                                     gTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGcgcgcg                                                                                             <  1:72536/76‑1 (MQ=255)
                                                                                                     gTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGcgcgcg                                                                                             >  2:72536/1‑76 (MQ=255)
                                                                                                       gAATTATCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTg                            <  1:1377554/139‑1 (MQ=255)
                                                                                                            aTCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGt                       >  1:737300/1‑139 (MQ=255)
                                                                                                             tCAGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTa                      >  1:1329195/1‑139 (MQ=255)
                                                                                                               aGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGa                                                                                                                          <  2:1428696/37‑1 (MQ=255)
                                                                                                               aGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGa                                                                                                                          >  1:1428696/1‑37 (MQ=255)
                                                                                                               aGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAgggg                                                                                                   <  1:329120/60‑1 (MQ=255)
                                                                                                               aGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAgggg                                                                                                   >  2:329120/1‑60 (MQ=255)
                                                                                                               aGCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTaaa                    >  2:152025/1‑139 (MQ=255)
                                                                                                                gCGGGCGCTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTAAAt                   >  2:1439993/1‑139 (MQ=255)
                                                                                                                    gcgcTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAAc                                                   >  2:498695/1‑103 (MQ=255)
                                                                                                                    gcgcTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAAc                                                   <  1:498695/103‑1 (MQ=255)
                                                                                                                    gcgcTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATcccc                                         >  2:671201/1‑113 (MQ=255)
                                                                                                                    gcgcTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATcccc                                         <  1:671201/113‑1 (MQ=255)
                                                                                                                    gcgcTGGAAGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTAAATCTGt               >  1:541588/1‑139 (MQ=255)
                                                                                                                           aaGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGa                                                     >  2:1286494/1‑94 (MQ=255)
                                                                                                                           aaGGCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGa                                                     <  1:1286494/94‑1 (MQ=255)
                                                                                                                              gCGAGCTTCCTCGTACCATCGAAACTATCGGCCCGGTAAAGGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCGTTCTGCATCGGTGACGGTAAATCTGTTACCCGGCcg     <  1:263568/139‑1 (MQ=255)
                                                                                                                                 aGCTTCCTCGTACCATCGAAACTATCGGTCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTAAATCTGTTACCCGGCCgcgc  <  1:905307/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                     
TGCGTCTGCGCCTGGCACAACAAGGTTTGCCAAAAGGCGGCGCGGTCGGTTTCGAACTGCTTGATCAGGAAAAGTTTGGTATCAGCCAGTTCAGCGAACAGGTGAATTATCAGCGGGCGCTGGAAGGCGAGCTTTCTCGTACCATCGAAACTATCGGCCCGGTAAAAGGGGCGCGCGTACATCTGGCAATGCCGAAACCGTCTTTATTCGTCCGTGAACAAAAATCCCCTTCTGCATCGGTGACGGTAAATCTGTTACCCGGCCGCGC  >  NC_000913/2013506‑2013773

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A