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 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,102,221 T→C E107E (GAA→GAG)  csgE ← curlin secretion specificity factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,102,2210TC100.0% 192.0 / NA 53E107E (GAA→GAG) csgEcurlin secretion specificity factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/26);  total (27/26)

CGAAATAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCTTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCACTG  >  NC_000913/1102086‑1102347
                                                                                                                                       |                                                                                                                              
cGAAATAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctct                                                                                                                             >  2:985882/1‑139 (MQ=255)
 gAAATAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctctt                                                                                                                            <  2:1244409/139‑1 (MQ=255)
   aaTAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctctt                                                                                                                            <  2:321842/137‑1 (MQ=255)
   aaTAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctctt                                                                                                                            >  1:321842/1‑137 (MQ=255)
             aGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCa                                                                                                                >  1:602231/1‑139 (MQ=255)
                  aaCTACTGCATGTTTGACACGCATTGCTGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  <  1:966393/132‑1 (MQ=255)
                  aaCTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  >  2:966393/1‑132 (MQ=255)
                       ctGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAgac                                                                                                      >  2:304277/1‑139 (MQ=255)
                         gCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAgacga                                                                                                    >  2:1354307/1‑139 (MQ=255)
                                          tGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGtct                                                                                   <  1:1354307/139‑1 (MQ=255)
                                                 tCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctctt                                                                                                                            >  2:1099768/1‑91 (MQ=255)
                                                 tCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGcctctt                                                                                                                            <  1:1099768/91‑1 (MQ=255)
                                                 tCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCa                                                                            >  1:77775/1‑139 (MQ=255)
                                                     aaCAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACgg                                                                        <  1:1008/139‑1 (MQ=255)
                                                            ttttATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATaaa                                                                 <  1:304277/139‑1 (MQ=255)
                                                                          catcatGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAAt                                                   <  2:602231/139‑1 (MQ=255)
                                                                           atcatGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATa                                                  >  1:1092419/1‑139 (MQ=255)
                                                                                gcgcCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTc                                             >  2:20778/1‑139 (MQ=255)
                                                                                     aaaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  >  2:1446877/1‑65 (MQ=255)
                                                                                     aaaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  >  2:833894/1‑65 (MQ=255)
                                                                                     aaaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  <  1:833894/65‑1 (MQ=255)
                                                                                     aaaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  <  1:1446877/65‑1 (MQ=255)
                                                                                      aaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGAtt                                       <  2:77775/139‑1 (MQ=255)
                                                                                      aaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGAtt                                       <  1:788600/139‑1 (MQ=255)
                                                                                      aaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGAtt                                       >  1:856734/1‑139 (MQ=255)
                                                                                      aaTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGAtt                                       <  2:856734/139‑1 (MQ=255)
                                                                                       aTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTGAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCaa                                                                           >  2:169964/1‑102 (MQ=255)
                                                                                       aTCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTGAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCaa                                                                           <  1:169964/102‑1 (MQ=255)
                                                                                             cGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAAc                                                                          >  1:1218205/1‑97 (MQ=255)
                                                                                             cGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAAc                                                                          <  2:1218205/97‑1 (MQ=255)
                                                                                                    aataaCGCCTGATTTATCTGGCGACGA‑TTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGa                                                                                        <  1:1407457/75‑1 (MQ=255)
                                                                                                    aataaCGCCTGATTTATCTGGCGACGA‑TTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGa                                                                                        >  2:1407457/1‑75 (MQ=255)
                                                                                                      taaCGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATaaaaaa                                                              <  2:163501/100‑1 (MQ=255)
                                                                                                      taaCGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATaaaaaa                                                              >  1:163501/1‑100 (MQ=255)
                                                                                                         cGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACgg                                                                        >  1:67999/1‑87 (MQ=255)
                                                                                                         cGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACgg                                                                        <  2:67999/87‑1 (MQ=255)
                                                                                                         cGCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTCTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAg                    >  2:913314/1‑139 (MQ=255)
                                                                                                          gCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGAc                                    <  1:88435/122‑1 (MQ=255)
                                                                                                          gCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGAc                                    >  2:88435/1‑122 (MQ=255)
                                                                                                          gCCTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGc                   >  1:505686/1‑139 (MQ=255)
                                                                                                           ccTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAGAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTc                                                           >  1:149187/1‑98 (MQ=255)
                                                                                                           ccTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAGAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTc                                                           <  2:149187/98‑1 (MQ=255)
                                                                                                           ccTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGACAATAACGTCCTGATTGACCg                                  >  1:945289/1‑123 (MQ=255)
                                                                                                           ccTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCg                                  <  2:945289/123‑1 (MQ=255)
                                                                                                            cTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  <  1:418477/42‑1 (MQ=255)
                                                                                                            cTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAAt                                                                                                                  >  2:418477/1‑42 (MQ=255)
                                                                                                            cTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGt                                                            >  1:1293225/1‑96 (MQ=255)
                                                                                                            cTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGt                                                            <  2:1293225/96‑1 (MQ=255)
                                                                                                            cTGATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCtt                 >  1:599337/1‑139 (MQ=255)
                                                                                                              gATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTcc               <  1:20778/139‑1 (MQ=255)
                                                                                                              gATTTATCTGGCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTcc               <  1:913314/139‑1 (MQ=255)
                                                                                                                        gCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCa     >  1:1330629/1‑139 (MQ=255)
                                                                                                                        gCGACGATTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCa     <  2:1092419/139‑1 (MQ=255)
                                                                                                                         cgacgaTTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGa                                         >  2:841400/1‑102 (MQ=255)
                                                                                                                         cgacgaTTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGa                                         <  1:841400/102‑1 (MQ=255)
                                                                                                                          gacgaTTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCACt   <  2:599337/139‑1 (MQ=255)
                                                                                                                           acgaTTTAGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCACTg  >  2:693941/1‑139 (MQ=255)
                                                                                                                                  aGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGAc                                    <  2:36748/98‑1 (MQ=255)
                                                                                                                                  aGTGCCTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGAc                                    >  1:36748/1‑98 (MQ=255)
                                                                                                                                       |                                                                                                                              
CGAAATAAGCATGAGTAGAACTACTGCATGTTTGACACGCATTGCAGCCTCCGAACAATTTTTTATTTAGAATTCATCATGCGCCAAATCGCCCGTACTTAATAACGCCTGATTTATCTGGCGACGATTTAGTGCTTCTTCAGTTTGAATCAGTGCAAAGACGACAGTTTTCTCGAAGTCTCTTTTCAACGGAAATAAAAAAGTCTGGAAAATAACGTCCTGATTGACCGTTATAGTGATCCAGCTTCCCCATCGTGCACTG  >  NC_000913/1102086‑1102347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A