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
A35 F9 I0 R1 1164 192.0 7567036 97.0% 7340024 130.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,530,490 T→C 7.3% intergenic (+86/‑96) ydcD → / → yncI putative immunity protein for RhsE/pseudogene

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,530,4900TC 7.3% 177.3 / 4.3 55intergenic (+86/‑96)ydcD/yncIputative immunity protein for RhsE/pseudogene
Reads supporting (aligned to +/- strand):  ref base T (25/26);  new base C (2/2);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

ATTATTATGATAACAATTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAGTATTCAAAGTTTGCTTGATTATATTTCA  >  NC_000913/1530346‑1530618
                                                                                                                                                |                                                                                                                                
attattATGATAACAATTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGa                                                                                                                              <  1:1785967/149‑1 (MQ=255)
          tAACAATTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGAGATGAGAGCAAGGGAGGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCAc                                                                                                                    >  4:1011381/1‑149 (MQ=255)
            aCAATTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGa                                                                                                                  >  2:1138325/1‑149 (MQ=255)
              aaTTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     >  1:1160756/1‑144 (MQ=255)
              aaTTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     <  2:1160756/144‑1 (MQ=255)
               aTTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGAttt                                                                                                               <  3:103310/149‑1 (MQ=255)
                 ttGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGa                                                                                                                              <  1:1171179/132‑1 (MQ=255)
                 ttGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGa                                                                                                                              >  2:1171179/1‑132 (MQ=255)
                      aaaTGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGt                                                                                                                           >  2:1318051/1‑130 (MQ=255)
                      aaaTGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGt                                                                                                                           <  1:1318051/130‑1 (MQ=255)
                       aaTGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     >  3:129577/1‑135 (MQ=255)
                       aaTGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCttt                                                                                                       <  1:1138325/149‑1 (MQ=255)
                       aaTGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAACACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     <  4:129577/135‑1 (MQ=255)
                              tttttGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtg                                                                                                                                 >  2:1640235/1‑116 (MQ=255)
                              tttttGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtg                                                                                                                                 <  1:1640235/116‑1 (MQ=255)
                              tttttGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTTATGTAAATCACGATTTTCATCTTTGCTTTaa                                                                                                <  3:1011381/149‑1 (MQ=255)
                              tttttGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATCGTGATTTACATCAcaa                                                                                                                  <  3:656215/131‑3 (MQ=255)
                              tttttGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATCGTGATTTACATCAcaa                                                                                                                  >  4:656215/1‑129 (MQ=255)
                                      tGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGcc                                                                                            <  1:607657/145‑1 (MQ=255)
                                      tGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGcc                                                                                            >  2:607657/1‑145 (MQ=255)
                                          ttGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGc                                                                                             >  4:1487903/1‑140 (MQ=255)
                                          ttGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGc                                                                                             <  3:1487903/140‑1 (MQ=255)
                                             gTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATc                                                                                 >  2:1163333/1‑149 (MQ=255)
                                               aaaTGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATCGTGATTTACATCACAAtt                                                                                                                <  2:1860249/116‑1 (MQ=255)
                                               aaaTGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATCGTGATTTACATCACAAtt                                                                                                                >  1:1860249/1‑116 (MQ=255)
                                                             aacaacACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTgg                                                                 >  4:290363/1‑149 (MQ=255)
                                                                aacaCCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAAt                                                              >  3:943960/1‑149 (MQ=255)
                                                                   acCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtgt                                                                                                                                >  4:848770/1‑80 (MQ=255)
                                                                   acCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtgt                                                                                                                                <  3:848770/80‑1 (MQ=255)
                                                                     cAGAAAGAGAAAGAGATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     >  3:137988/1‑89 (MQ=255)
                                                                     cAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCa                                                                                                                     <  4:137988/89‑1 (MQ=255)
                                                                      aGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGAtt                                                                                                                >  1:1716831/1‑93 (MQ=255)
                                                                      aGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGAtt                                                                                                                <  2:1716831/93‑1 (MQ=255)
                                                                         aaGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTaaaaa                                                     <  4:943960/149‑1 (MQ=255)
                                                                         aaGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTaaaaa                                                     <  1:1163333/149‑1 (MQ=255)
                                                                                  atatAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATaaaaaa                                            <  3:290363/149‑1 (MQ=255)
                                                                                          tacatacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCttt                                                                   <  1:1150341/118‑1 (MQ=255)
                                                                                          tacatacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCttt                                                                   >  2:928536/1‑118 (MQ=255)
                                                                                          tacatacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCttt                                                                   >  2:1150341/1‑118 (MQ=255)
                                                                                          tacatacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCttt                                                                   <  1:928536/118‑1 (MQ=255)
                                                                                              tacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATaa                                                            >  2:1780103/1‑121 (MQ=255)
                                                                                              tacaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATaa                                                            <  1:1780103/121‑1 (MQ=255)
                                                                                               acaGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGa                               >  3:842206/1‑149 (MQ=255)
                                                                                                 aGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtg                                                                                                                                 <  2:4589/49‑1 (MQ=255)
                                                                                                 aGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATtg                                                                                                                                 >  1:4589/1‑49 (MQ=255)
                                                                                                  gAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAg                              <  4:457453/147‑1 (MQ=255)
                                                                                                  gAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAg                              >  3:457453/1‑147 (MQ=255)
                                                                                                         aTGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATc                                                                                 >  3:225867/1‑89 (MQ=255)
                                                                                                         aTGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATc                                                                                 <  4:225867/89‑1 (MQ=255)
                                                                                                                  aGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  <  1:1166367/95‑1 (MQ=255)
                                                                                                                  aGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  <  1:1689965/95‑1 (MQ=255)
                                                                                                                  aGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  >  2:1166367/1‑95 (MQ=255)
                                                                                                                  aGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  >  2:1689965/1‑95 (MQ=255)
                                                                                                                   gggACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAGTATTCAAAGTTTGCTTGAt           >  4:1580466/1‑149 (MQ=255)
                                                                                                                     gACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAg                                           >  4:1834741/1‑115 (MQ=255)
                                                                                                                     gACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAg                                           <  3:1834741/115‑1 (MQ=255)
                                                                                                                            cagggcaAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAGTATTCAAAGTTTGCTTGATTATATTTCa  <  3:1580466/149‑1 (MQ=255)
                                                                                                                                 caAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  >  4:281969/1‑80 (MQ=255)
                                                                                                                                 caAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTg                                                                  <  3:281969/80‑1 (MQ=255)
                                                                                                                                            aaaTTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCa                                    >  2:1185124/1‑99 (MQ=255)
                                                                                                                                            aaaTTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCa                                    <  1:1185124/99‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                
ATTATTATGATAACAATTTGAAAAATGAAGTTTTTGACTGGATTGGTAAATGGTCATAATGAACAACACCAGAAAGAGAAAAATATAAAATACATACAGAAAGACATGAGAGCAAGGGACGGGGCAGGGCAAGATCATGAAAATTGTGATGTAAATCACGATTTTCATCTTTGCTTTAACGCCTACAGGTGATCAAAATTTAACCTTTGGAATAACTAAAAAGATAAAAAAGGACGCCAGGTGAGTATTCAAAGTTTGCTTGATTATATTTCA  >  NC_000913/1530346‑1530618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A