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 F50 I2 R1 209 44.2 1360995 98.7% 1343302 150.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,616,013 T→C intergenic (‑132/‑81) yfgO ← / → bepA putative UPF0118 family inner membrane permease/OM protein maintenance and assembly metalloprotease and chaperone, periplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,616,0130TC98.2% 199.3 / ‑4.0 54intergenic (‑132/‑81)yfgO/bepAputative UPF0118 family inner membrane permease/OM protein maintenance and assembly metalloprotease and chaperone, periplasmic
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (27/26);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.67e-01

CATTTCGAGCATAAAGACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTTACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATGACCATTGGTCAGGTA  >  NC_000913/2615870‑2616159
                                                                                                                                               |                                                                                                                                                  
cATTTCGAGCATAAAGACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTc                                                                                                                                              >  1:56139/1‑150 (MQ=255)
   ttCGAGCATAAAGACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCaaa                                                                                                                                           <  2:110322/150‑1 (MQ=255)
          aTAAAGACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGgcgc                                                                                                                                   >  1:487830/1‑151 (MQ=255)
               gACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTgg                                                                                                                              <  1:340927/151‑1 (MQ=255)
                aCCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTggg                                                                                                                             >  1:81401/1‑151 (MQ=255)
                  cTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGa                                                                                                                            >  2:279774/1‑150 (MQ=255)
                     cccTTAACCTCAAGCGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACg                                                                                                                         >  1:116752/1‑150 (MQ=255)
                         gAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATAtt                                                                                                                    <  1:461375/151‑1 (MQ=255)
                         gAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATAtt                                                                                                                    >  2:54653/1‑151 (MQ=255)
                             cTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTcac                                                                                                                >  2:651783/1‑151 (MQ=255)
                                aaGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGt                                                                                                             >  2:17427/1‑151 (MQ=255)
                                 agagCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTa                                                                                                            <  1:575350/151‑1 (MQ=255)
                                  gagCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTAt                                                                                                           >  1:462327/1‑151 (MQ=255)
                                   agCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATc                                                                                                          <  2:64441/151‑1 (MQ=255)
                                       ggATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTc                                                                                                      <  1:278138/151‑1 (MQ=255)
                                         aTTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCa                                                                                                     >  2:403377/1‑150 (MQ=255)
                                            gCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATg                                                                                                 <  2:105908/151‑1 (MQ=255)
                                             cGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGa                                                                                                <  1:419488/151‑1 (MQ=255)
                                               aTCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACt                                                                                              <  2:113960/151‑1 (MQ=255)
                                                tCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACt                                                                                              >  2:550191/1‑150 (MQ=255)
                                                      aTTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCa                                                                                       <  1:29832/151‑1 (MQ=255)
                                                           aTCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAAt                                                                                  >  2:59782/1‑151 (MQ=255)
                                                                      acaAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATag                                                                         >  1:177722/1‑149 (MQ=255)
                                                                           aaaGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTAt                                                                  <  1:100857/151‑1 (MQ=255)
                                                                           aaaGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTAt                                                                  <  1:26464/151‑1 (MQ=255)
                                                                             aGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGt                                                                >  2:491278/1‑151 (MQ=255)
                                                                                 ttCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTc                                                              >  2:14989/1‑149 (MQ=255)
                                                                                  tCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCa                                                             <  2:214653/149‑1 (MQ=255)
                                                                                          tATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGa                                                    >  2:519056/1‑150 (MQ=255)
                                                                                          tATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGa                                                    >  2:358819/1‑150 (MQ=255)
                                                                                           aTGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTTACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGaa                                                   <  2:626707/150‑1 (MQ=255)
                                                                                           aTGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGaa                                                   <  2:368802/150‑1 (MQ=255)
                                                                                            tGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGaaa                                                  >  2:629916/1‑150 (MQ=255)
                                                                                             gACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGaaaaa                                                <  2:12128/151‑1 (MQ=255)
                                                                                               cGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGaaaaaaa                                              <  2:511628/151‑1 (MQ=255)
                                                                                                  aTTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAAcc                                           <  1:185542/151‑1 (MQ=255)
                                                                                                       ggAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGtt                                      >  2:639501/1‑151 (MQ=255)
                                                                                                         aaaCTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGc                                    >  1:528005/1‑151 (MQ=255)
                                                                                                          aaCTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAATCCTGGTTGCa                                   <  2:655241/151‑1 (MQ=255)
                                                                                                          aaCTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGc                                    >  1:154343/1‑150 (MQ=255)
                                                                                                          aaCTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCa                                   <  2:656353/151‑1 (MQ=255)
                                                                                                           aCTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCaa                                  <  1:375702/151‑1 (MQ=255)
                                                                                                            cTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAAc                                 >  2:591243/1‑151 (MQ=255)
                                                                                                              gAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCaaa                                 <  1:175883/149‑2 (MQ=255)
                                                                                                              gAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAAcc                                <  1:488338/150‑1 (MQ=255)
                                                                                                                aaaGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTc                             >  2:499586/1‑151 (MQ=255)
                                                                                                                 aaGTCATTTGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTc                             >  1:290490/1‑150 (MQ=255)
                                                                                                                        ttGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATtgctgc                     >  2:136266/1‑151 (MQ=255)
                                                                                                                        ttGAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATtgctg                      <  2:273730/150‑1 (MQ=255)
                                                                                                                          gAGTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTgctgct                    <  1:499940/150‑1 (MQ=255)
                                                                                                                            gTGGGCTAATCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATg                 <  2:363106/151‑1 (MQ=255)
                                                                                                                                     tCTTCGCCGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATGACCATTGGt        >  1:225840/1‑151 (MQ=255)
                                                                                                                                           ccGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATGACCATTGGTCAGGTa  <  1:27326/151‑1 (MQ=255)
                                                                                                                                            cGTCACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATGACCATTGGTCAGGt   >  2:310558/1‑149 (MQ=255)
                                                                                                                                               |                                                                                                                                                  
CATTTCGAGCATAAAGACCTTCCCTGAACCTCAAGAGCGGGATTGCGATCCGCAATTGTATCGAAATGTCACAAAAAAGACTTCGCTTTTTATGACGGATTCAGGAAACTGAAAAGTCATTTGAGTGGGCTAATCTTCGCCGTTACACTCAAAGGCGGCGCGGTGGGAACGATATTTCACAGTATCGGTCAAATGACTATCTCCAGAAATACAGGATAGAGGTTATGTTCAGGCAGTTGAAAAAAAACCTGGTTGCAACCCTCATTGCTGCTATGACCATTGGTCAGGTA  >  NC_000913/2615870‑2616159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A